From f1ce9040ce6864dbbfc63c10899d42ceca58eb29 Mon Sep 17 00:00:00 2001 From: Bess Sadler Date: Mon, 17 Jun 2024 10:14:21 -0400 Subject: [PATCH] Remove data migration specs used early in the project (#1842) Co-authored-by: Hector Correa --- spec/system/data_migration/attention.xml | 80 -------- .../attention_form_submission_spec.rb | 89 --------- spec/system/data_migration/baldwin.xml | 81 -------- .../baldwin_form_submission_spec.rb | 83 -------- spec/system/data_migration/bitklavier.xml | 55 ------ .../bitklavier_form_submission_spec.rb | 74 ------- .../system/data_migration/bitklavierimage.xml | 69 ------- .../bitklavierimage_form_submission_spec.rb | 90 --------- spec/system/data_migration/cklibrary.xml | 69 ------- .../cklibrary_form_submission_spec.rb | 73 ------- spec/system/data_migration/cytoskeletal.xml | 117 ------------ .../cytoskeletal_form_submission_spec.rb | 133 ------------- .../data_migration/design_arrangment.xml | 95 --------- .../design_arrangment_form_submission_spec.rb | 109 ----------- .../system/data_migration/dynamic_tension.xml | 96 ---------- .../dynamic_tension_form_submission_spec.rb | 102 ---------- .../system/data_migration/electromagnetic.xml | 103 ---------- .../electromagnetic_form_submission_spec.rb | 105 ---------- spec/system/data_migration/femtosecond.xml | 180 ------------------ .../femtosecond_form_submission_spec.rb | 163 ---------------- spec/system/data_migration/flume.xml | 60 ------ .../flume_form_submission_spec.rb | 75 -------- spec/system/data_migration/fusion_energy.xml | 69 ------- .../fusion_energy_form_submission_spec.rb | 85 --------- spec/system/data_migration/hybrid_drift.xml | 143 -------------- .../hybrid_drift_form_submission_spec.rb | 156 --------------- spec/system/data_migration/ion_orbital.xml | 97 ---------- .../ion_orbital_form_submission_spec.rb | 99 ---------- .../data_migration/non_axisymmetric.xml | 92 --------- .../non_axisymmetric_form_submission_spec.rb | 108 ----------- .../observation_axisymmetric.xml | 78 -------- ...ation_axisymmetric_form_submission_spec.rb | 100 ---------- spec/system/data_migration/sowingseeds.xml | 76 -------- .../sowingseeds_form_submission_spec.rb | 93 --------- spec/system/data_migration/spindle.xml | 66 ------- .../spindle_form_submission_spec.rb | 79 -------- .../data_migration/thomson_scattering.xml | 131 ------------- ...thomson_scattering_form_submission_spec.rb | 139 -------------- 38 files changed, 3712 deletions(-) delete mode 100644 spec/system/data_migration/attention.xml delete mode 100644 spec/system/data_migration/attention_form_submission_spec.rb delete mode 100644 spec/system/data_migration/baldwin.xml delete mode 100644 spec/system/data_migration/baldwin_form_submission_spec.rb delete mode 100644 spec/system/data_migration/bitklavier.xml delete mode 100644 spec/system/data_migration/bitklavier_form_submission_spec.rb delete mode 100644 spec/system/data_migration/bitklavierimage.xml delete mode 100644 spec/system/data_migration/bitklavierimage_form_submission_spec.rb delete mode 100644 spec/system/data_migration/cklibrary.xml delete mode 100644 spec/system/data_migration/cklibrary_form_submission_spec.rb delete mode 100644 spec/system/data_migration/cytoskeletal.xml delete mode 100644 spec/system/data_migration/cytoskeletal_form_submission_spec.rb delete mode 100644 spec/system/data_migration/design_arrangment.xml delete mode 100644 spec/system/data_migration/design_arrangment_form_submission_spec.rb delete mode 100644 spec/system/data_migration/dynamic_tension.xml delete mode 100644 spec/system/data_migration/dynamic_tension_form_submission_spec.rb delete mode 100644 spec/system/data_migration/electromagnetic.xml delete mode 100644 spec/system/data_migration/electromagnetic_form_submission_spec.rb delete mode 100644 spec/system/data_migration/femtosecond.xml delete mode 100644 spec/system/data_migration/femtosecond_form_submission_spec.rb delete mode 100644 spec/system/data_migration/flume.xml delete mode 100644 spec/system/data_migration/flume_form_submission_spec.rb delete mode 100644 spec/system/data_migration/fusion_energy.xml delete mode 100644 spec/system/data_migration/fusion_energy_form_submission_spec.rb delete mode 100644 spec/system/data_migration/hybrid_drift.xml delete mode 100644 spec/system/data_migration/hybrid_drift_form_submission_spec.rb delete mode 100644 spec/system/data_migration/ion_orbital.xml delete mode 100644 spec/system/data_migration/ion_orbital_form_submission_spec.rb delete mode 100644 spec/system/data_migration/non_axisymmetric.xml delete mode 100644 spec/system/data_migration/non_axisymmetric_form_submission_spec.rb delete mode 100644 spec/system/data_migration/observation_axisymmetric.xml delete mode 100644 spec/system/data_migration/observation_axisymmetric_form_submission_spec.rb delete mode 100644 spec/system/data_migration/sowingseeds.xml delete mode 100644 spec/system/data_migration/sowingseeds_form_submission_spec.rb delete mode 100644 spec/system/data_migration/spindle.xml delete mode 100644 spec/system/data_migration/spindle_form_submission_spec.rb delete mode 100644 spec/system/data_migration/thomson_scattering.xml delete mode 100644 spec/system/data_migration/thomson_scattering_form_submission_spec.rb diff --git a/spec/system/data_migration/attention.xml b/spec/system/data_migration/attention.xml deleted file mode 100644 index c5c06537b..000000000 --- a/spec/system/data_migration/attention.xml +++ /dev/null @@ -1,80 +0,0 @@ - - 10.34770/9425-b553 - - - Wilterson, Andrew - Andrew - Wilterson - 0000-0002-4080-5386 - - - Nastase, Samuel - Samuel - Nastase - 0000-0001-7013-5275 - - - Bio, Branden - Branden - Bio - 0000-0002-6243-3165 - - - Guterstam, Arvid - Arvid - Guterstam - 0000-0002-3694-1318 - - - Graziano, Michael - Michael - Graziano - - - - Attention and awareness in the dorsal attention network - - Princeton University - - 2020 - - - Princeton Neuroscience Institute Innovation Fund - PRINU-24400-G0002-10005089-101 - - - - ark:/88435/dsp01xp68kk27p - - 1 - - Creative Commons Attribution 4.0 International - - - - The attention schema theory (AST) posits a specific relationship between - subjective awareness and attention, in which awareness is the control - model that the brain uses to aid in the endogenous control of attention. - We proposed that the right temporoparietal junction (TPJ) is involved in - that interaction between awareness and attention. In previous experiments, - we developed a behavioral paradigm in human subjects to manipulate - awareness and attention. The paradigm involved a visual cue that could be - used to guide a shift of attention to a target stimulus. In task 1, - subjects were aware of the visual cue, and their endogenous control - mechanism was able to use the cue to help control attention. In task 2, - subjects were unaware of the visual cue, and their endogenous control - mechanism was no longer able to use it to control attention, even though - the cue still had a measurable effect on other aspects of behavior. Here - we tested the two tasks while scanning brain activity in human volunteers. - We predicted that the right TPJ would be active in relation to the cue in - task 1, but not in task 2. This prediction was confirmed. The right TPJ - was active in relation to the cue in task 1; it was not measurably active - in task 2; the difference was significant. In our interpretation, the - right TPJ is involved in a complex interaction in which awareness aids in - the control of attention. This dataset contains structural and functional - MRI images from human subjects learning to use subliminal and superliminal - stimuli to perform a Posner-like reaction time task. Download the - README.txt file for a detailed description of this dataset's content - - - \ No newline at end of file diff --git a/spec/system/data_migration/attention_form_submission_spec.rb b/spec/system/data_migration/attention_form_submission_spec.rb deleted file mode 100644 index e441ca57d..000000000 --- a/spec/system/data_migration/attention_form_submission_spec.rb +++ /dev/null @@ -1,89 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating attention", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "Attention and awareness in the dorsal attention network" } - let(:description) do - "The attention schema theory (AST) posits a specific relationship between subjective awareness and attention, in which awareness is the control model that the brain uses to aid in the endogenous control of attention. We proposed that the right temporoparietal junction (TPJ) is involved in that interaction between awareness and attention. In previous experiments, we developed a behavioral paradigm in human subjects to manipulate awareness and attention. The paradigm involved a visual cue that could be used to guide a shift of attention to a target stimulus. In task 1, subjects were aware of the visual cue, and their endogenous control mechanism was able to use the cue to help control attention. In task 2, subjects were unaware of the visual cue, and their endogenous control mechanism was no longer able to use it to control attention, even though the cue still had a measurable effect on other aspects of behavior. Here we tested the two tasks while scanning brain activity in human volunteers. We predicted that the right TPJ would be active in relation to the cue in task 1, but not in task 2. This prediction was confirmed. The right TPJ was active in relation to the cue in task 1; it was not measurably active in task 2; the difference was significant. In our interpretation, the right TPJ is involved in a complex interaction in which awareness aids in the control of attention. This dataset contains structural and functional MRI images from human subjects learning to use subliminal and superliminal stimuli to perform a Posner-like reaction time task. Download the README.txt file for a detailed description of this dataset's content" - end - let(:ark) { "ark:/88435/dsp01xp68kk27p" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/9425-b553" } - let(:file_upload) { Pathname.new(fixture_path).join("dataspace_migration", "attention", "Attention_Awareness_Dorsal_Attention_README.txt").to_s } - let(:file1) { FactoryBot.build :s3_file, filename: file_upload } - let(:bucket_url) { @bucket_url } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/9425-b553") - .to_return(status: 200, body: "", headers: {}) - stub_request(:get, /#{bucket_url}/).to_return(status: 200) - stub_request(:put, /#{bucket_url}/).to_return(status: 200) - stub_s3(data: [file1]) - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-4080-5386" - find("tr:last-child input[name='creators[][given_name]']").set "Andrew" - find("tr:last-child input[name='creators[][family_name]']").set "Wilterson" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-7013-5275" - find("tr:last-child input[name='creators[][given_name]']").set "Samuel" - find("tr:last-child input[name='creators[][family_name]']").set "Nastase" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-6243-3165" - find("tr:last-child input[name='creators[][given_name]']").set "Branden" - find("tr:last-child input[name='creators[][family_name]']").set "Bio" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-3694-1318" - find("tr:last-child input[name='creators[][given_name]']").set "Arvid" - find("tr:last-child input[name='creators[][family_name]']").set "Guterstam" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Michael" - find("tr:last-child input[name='creators[][family_name]']").set "Graziano" - - click_on "Additional Metadata" - - ## Funder Information - # An example of a funder who does not have an ROR - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][funder_name]']").set "Princeton Neuroscience Institute Innovation Fund" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "PRINU-24400-G0002-10005089-101" - - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2020 - select "Research Data", from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - attach_file_via_uppy(file_upload) - - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - attention_work = Work.last - expect(attention_work.title).to eq title - expect(attention_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(attention_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/attention.xml")) - export_spec_data("attention.json", attention_work.to_json) - end - end -end diff --git a/spec/system/data_migration/baldwin.xml b/spec/system/data_migration/baldwin.xml deleted file mode 100644 index 266d4f979..000000000 --- a/spec/system/data_migration/baldwin.xml +++ /dev/null @@ -1,81 +0,0 @@ - - 10.34770/xajd-5n64 - - - Baldwin, Jane W - Jane W - Baldwin - 0000-0002-4174-2743 - - - Dessy, Jay Benjamin - Jay Benjamin - Dessy - 0000-0003-0053-7409 - - - Vecchi, Gabriel A - Gabriel A - Vecchi - 0000-0002-5085-224X - - - Oppenheimer, Michael - Michael - Oppenheimer - 0000-0002-9708-5914 - - - Jia, Liwei - Liwei - Jia - - - Gudgel, Richard G - Richard G - Gudgel - - - Paffendorf, Karen - Karen - Paffendorf - 0000-0003-0657-3515 - - - - - Supporting data for Baldwin et al 2019 "Temporally Compound Heat - Waves and Global Warming: An Emerging Hazard" - - - Princeton University - - 2019 - - ark:/88435/dsp01bz60d033c - - 1 - - Creative Commons Attribution 4.0 International - - - - This data is compiled to support a publication in the journal Earth's - Future: Baldwin et al 2019 "Temporally Compound Heat Waves and Global - Warming: An Emerging Hazard". The GCM GFDL CM2.5-FLOR was used to - produce the raw climate model data. The model code for FLOR is freely - available and can be downloaded at - https://www.gfdl.noaa.gov/cm2-5-and-flor/. Code used to calculate the - derived heat wave statistics data and produce figures in the paper is - available at https://github.com/janewbaldwin/Compound-Heat-Waves The heat - wave statistics derived output for only one definition is provided (daily - minimum temperature, 90th percentile threshold, temporal structure 3114) - which is the definition used the most in the paper figures. Statistics for - the other definitions can be created by running the HWSTATS code provided - in the corresponding github folder, which includes python scripts which do - the analysis and PBS job scheduling and submission scripts which show how - to run the python scripts. For more information on this, please see the - github readme. - - - \ No newline at end of file diff --git a/spec/system/data_migration/baldwin_form_submission_spec.rb b/spec/system/data_migration/baldwin_form_submission_spec.rb deleted file mode 100644 index d0bf396f1..000000000 --- a/spec/system/data_migration/baldwin_form_submission_spec.rb +++ /dev/null @@ -1,83 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating baldwin", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "Supporting data for Baldwin et al 2019 \"Temporally Compound Heat Waves and Global Warming: An Emerging Hazard\"" } - let(:description) do - "This data is compiled to support a publication in the journal Earth's Future: Baldwin et al 2019 \"Temporally Compound Heat Waves and Global Warming: An Emerging Hazard\". The GCM GFDL CM2.5-FLOR was used to produce the raw climate model data. The model code for FLOR is freely available and can be downloaded at https://www.gfdl.noaa.gov/cm2-5-and-flor/. Code used to calculate the derived heat wave statistics data and produce figures in the paper is available at https://github.com/janewbaldwin/Compound-Heat-Waves The heat wave statistics derived output for only one definition is provided (daily minimum temperature, 90th percentile threshold, temporal structure 3114) which is the definition used the most in the paper figures. Statistics for the other definitions can be created by running the HWSTATS code provided in the corresponding github folder, which includes python scripts which do the analysis and PBS job scheduling and submission scripts which show how to run the python scripts. For more information on this, please see the github readme." - end - let(:ark) { "ark:/88435/dsp01bz60d033c" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/xajd-5n64" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/xajd-5n64") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-4174-2743" - find("tr:last-child input[name='creators[][given_name]']").set "Jane W" - find("tr:last-child input[name='creators[][family_name]']").set "Baldwin" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-0053-7409" - find("tr:last-child input[name='creators[][given_name]']").set "Jay Benjamin" - find("tr:last-child input[name='creators[][family_name]']").set "Dessy" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-5085-224X" - find("tr:last-child input[name='creators[][given_name]']").set "Gabriel A" - find("tr:last-child input[name='creators[][family_name]']").set "Vecchi" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-9708-5914" - find("tr:last-child input[name='creators[][given_name]']").set "Michael" - find("tr:last-child input[name='creators[][family_name]']").set "Oppenheimer" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Liwei" - find("tr:last-child input[name='creators[][family_name]']").set "Jia" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Richard G" - find("tr:last-child input[name='creators[][family_name]']").set "Gudgel" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-0657-3515" - find("tr:last-child input[name='creators[][given_name]']").set "Karen" - find("tr:last-child input[name='creators[][family_name]']").set "Paffendorf" - click_on "Additional Metadata" - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2019 - fill_in "doi", with: doi - fill_in "ark", with: ark - select "Research Data", from: "group_id" - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - baldwin_work = Work.last - expect(baldwin_work.title).to eq title - expect(baldwin_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(baldwin_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/baldwin.xml")) - export_spec_data("baldwin.json", baldwin_work.to_json) - end - end -end diff --git a/spec/system/data_migration/bitklavier.xml b/spec/system/data_migration/bitklavier.xml deleted file mode 100644 index a15dc90c7..000000000 --- a/spec/system/data_migration/bitklavier.xml +++ /dev/null @@ -1,55 +0,0 @@ - - 10.34770/zztk-f783 - - - Trueman, Daniel - Daniel - Trueman - - - - bitKlavier Grand Sample Library—Binaural Mic Image - - Princeton University - - 2021 - - - Villalta, Andrés - - - Chou, Katie - - - Ayres, Christien - - - Wang, Matthew - - - - ark:/88435/dsp01nv9356017 - - 1 - - Creative Commons Attribution 4.0 International - - - - The bitKlavier Grand consists of sample collections of a new Steinway D - grand piano from nine different stereo mic images, with: 16 velocity - layers, at every minor 3rd (starting at A0); Hammer release samples; - Release resonance samples; Pedal samples. Release packages at 96k/24bit, - 88.2k/24bit, 48k/24bit, 44.1k/16bit are available for various - applications. Binaural: Neumann KU100 This is the binaural head placed in - the same location as a seated pianist. It accurately captures what the - player would hear while playing the instrument. File Naming Convention: C4 - = middle C. Main note names: [note name][octave]v[velocity].wav -- e.g., - “D#5v13.wav”. Release resonance notes: harm[note - name][octave]v[velocity].wav -- e.g., “harmC2v2.wav”. Hammer samples: - rel[1-88].wav (one per key) -- e.g., “rel23.wav”. Pedal samples: - pedal[D/U][velocity].wav -- e.g., “pedalU2.wav” => pedal release (U = - up), velocity = 2 (quicker release than velocity = 1). - - - \ No newline at end of file diff --git a/spec/system/data_migration/bitklavier_form_submission_spec.rb b/spec/system/data_migration/bitklavier_form_submission_spec.rb deleted file mode 100644 index 19d6a2fcb..000000000 --- a/spec/system/data_migration/bitklavier_form_submission_spec.rb +++ /dev/null @@ -1,74 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating bitklavier", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "bitKlavier Grand Sample Library—Binaural Mic Image" } - let(:description) do - "The bitKlavier Grand consists of sample collections of a new Steinway D grand piano from nine different stereo mic images, with: 16 velocity layers, at every minor 3rd (starting at A0); Hammer release samples; Release resonance samples; Pedal samples. Release packages at 96k/24bit, 88.2k/24bit, 48k/24bit, 44.1k/16bit are available for various applications. Binaural: Neumann KU100 This is the binaural head placed in the same location as a seated pianist. It accurately captures what the player would hear while playing the instrument. File Naming Convention: C4 = middle C. Main note names: [note name][octave]v[velocity].wav -- e.g., “D#5v13.wav”. Release resonance notes: harm[note name][octave]v[velocity].wav -- e.g., “harmC2v2.wav”. Hammer samples: rel[1-88].wav (one per key) -- e.g., “rel23.wav”. Pedal samples: pedal[D/U][velocity].wav -- e.g., “pedalU2.wav” => pedal release (U = up), velocity = 2 (quicker release than velocity = 1)." - end - let(:ark) { "ark:/88435/dsp01nv9356017" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/zztk-f783" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/zztk-f783") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][given_name]']").set "Daniel" - find("tr:last-child input[name='creators[][family_name]']").set "Trueman" - click_on "Additional Metadata" - find("tr:last-child input[name='contributors[][given_name]']").set "Matthew" - find("tr:last-child input[name='contributors[][family_name]']").set "Wang" - find("tr:last-child select[name='contributors[][role]']").find(:option, "Contact Person").select_option - click_on "Add Another Individual Contributor" - find("tr:last-child input[name='contributors[][given_name]']").set "Andrés" - find("tr:last-child input[name='contributors[][family_name]']").set "Villalta" - find("tr:last-child select[name='contributors[][role]']").find(:option, "Contact Person").select_option - click_on "Add Another Individual Contributor" - find("tr:last-child input[name='contributors[][given_name]']").set "Katie" - find("tr:last-child input[name='contributors[][family_name]']").set "Chou" - find("tr:last-child select[name='contributors[][role]']").find(:option, "Contact Person").select_option - click_on "Add Another Individual Contributor" - find("tr:last-child input[name='contributors[][given_name]']").set "Christien" - find("tr:last-child input[name='contributors[][family_name]']").set "Ayres" - find("tr:last-child select[name='contributors[][role]']").find(:option, "Contact Person").select_option - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2021 - select "Research Data", from: "group_id" - click_on "Curator Controlled" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - bitklavier_work = Work.last - expect(bitklavier_work.title).to eq title - expect(bitklavier_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(bitklavier_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/bitklavier.xml")) - export_spec_data("bitKlavier-binaural.json", bitklavier_work.to_json) - end - end -end diff --git a/spec/system/data_migration/bitklavierimage.xml b/spec/system/data_migration/bitklavierimage.xml deleted file mode 100644 index 9aff092d7..000000000 --- a/spec/system/data_migration/bitklavierimage.xml +++ /dev/null @@ -1,69 +0,0 @@ - - 10.34770/r75s-9j74 - - - Wang, Matthew - Matthew - Wang - - - Villalta, Andres - Andres - Villalta - - - Gordon, Jeffrey - Jeffrey - Gordon - - - Chou, Katie - Katie - Chou - - - Ayers, Christien - Christien - Ayers - - - Trueman, Daniel - Daniel - Trueman - - - - bitKlavier Grand Sample Library—Piano Bar Mic Image - - Princeton University - - 2021 - - ark:/88435/dsp015999n653h - - 1 - - Creative Commons Attribution 4.0 International - - - - The bitKlavier Grand consists of sample collections of a new Steinway D - grand piano from nine different stereo mic images, with: 16 velocity - layers, at every minor 3rd (starting at A0); Hammer release samples; - Release resonance samples; Pedal samples. Release packages at 96k/24bit, - 88.2k/24bit, 48k/24bit, 44.1k/16bit are available for various - applications. Piano Bar: Earthworks—omni-directionals. This microphone - system suspends omnidirectional microphones within the piano. The bar is - placed across the harp near the hammers and provides a low string / high - string player’s perspective. It also produces a close sound without room - or lid interactions. It can be panned across an artificial stereophonic - perspective effectively in post-production. File Naming Convention: C4 = - middle C. Main note names: [note name][octave]v[velocity].wav -- e.g., - “D#5v13.wav”. Release resonance notes: harm[note - name][octave]v[velocity].wav -- e.g., “harmC2v2.wav”. Hammer samples: - rel[1-88].wav (one per key) -- e.g., “rel23.wav”. Pedal samples: - pedal[D/U][velocity].wav -- e.g., “pedalU2.wav” => pedal release (U = - up), velocity = 2 (quicker release than velocity = 1). - - - \ No newline at end of file diff --git a/spec/system/data_migration/bitklavierimage_form_submission_spec.rb b/spec/system/data_migration/bitklavierimage_form_submission_spec.rb deleted file mode 100644 index 8356fbd03..000000000 --- a/spec/system/data_migration/bitklavierimage_form_submission_spec.rb +++ /dev/null @@ -1,90 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating bitklavierimage", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "bitKlavier Grand Sample Library—Piano Bar Mic Image" } - let(:description) do - "The bitKlavier Grand consists of sample collections of a new Steinway D grand piano from nine different stereo mic images, with: 16 velocity layers, at every minor 3rd (starting at A0); Hammer release samples; Release resonance samples; Pedal samples. -Release packages at 96k/24bit, 88.2k/24bit, 48k/24bit, 44.1k/16bit are available for various applications. -Piano Bar: Earthworks—omni-directionals. This microphone system suspends omnidirectional microphones within the piano. The bar is placed across the harp near the hammers and provides a low string / high string player’s perspective. It also produces a close sound without room or lid interactions. It can be panned across an artificial stereophonic perspective effectively in post-production. File Naming Convention: C4 = middle C. Main note names: [note name][octave]v[velocity].wav -- e.g., “D#5v13.wav”. Release resonance notes: harm[note name][octave]v[velocity].wav -- e.g., “harmC2v2.wav”. Hammer samples: rel[1-88].wav (one per key) -- e.g., “rel23.wav”. Pedal samples: pedal[D/U][velocity].wav -- e.g., “pedalU2.wav” => pedal release (U = up), velocity = 2 (quicker release than velocity = 1)." - end - let(:ark) { "ark:/88435/dsp015999n653h" } - let(:collection_tags) { ["bitklavier"] } - let(:group) { "Research Data" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/r75s-9j74" } - let(:keywords) { "bitKlavier, sample library, piano" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/r75s-9j74") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Matthew" - find("tr:last-child input[name='creators[][family_name]']").set "Wang" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Andres" - find("tr:last-child input[name='creators[][family_name]']").set "Villalta" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Jeffrey" - find("tr:last-child input[name='creators[][family_name]']").set "Gordon" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Katie" - find("tr:last-child input[name='creators[][family_name]']").set "Chou" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Christien" - find("tr:last-child input[name='creators[][family_name]']").set "Ayers" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Daniel" - find("tr:last-child input[name='creators[][family_name]']").set "Trueman" - click_on "Additional Metadata" - fill_in "keywords", with: keywords - # Select Additional Metadata Tab - click_on "Additional Metadata" - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2021 - fill_in "doi", with: doi - fill_in "ark", with: ark - select group, from: "group_id" - fill_in "collection_tags", with: collection_tags.join(", ") - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - bitklavierimage_work = Work.last - expect(bitklavierimage_work.title).to eq title - expect(bitklavierimage_work.resource.collection_tags).to eq collection_tags - expect(bitklavierimage_work.group).to eq Group.research_data - expect(bitklavierimage_work.ark).to eq ark - export_spec_data("bitklavier_image.json", bitklavierimage_work.to_json) - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(bitklavierimage_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/bitklavierimage.xml")) - end - end -end diff --git a/spec/system/data_migration/cklibrary.xml b/spec/system/data_migration/cklibrary.xml deleted file mode 100644 index d28af4dc5..000000000 --- a/spec/system/data_migration/cklibrary.xml +++ /dev/null @@ -1,69 +0,0 @@ - - 10.34770/doc-1 - - - Leach, Robert - Robert - Leach - - - Hecht, Michael - Michael - Hecht - - - Karas, Christina - Christina - Karas - - - - CKavity Library: Next-Generation Sequencing - - A library of novel genes with combinatorially diverse cavities, built on a - stably folded structural template - - - Princeton University - - 2019 - - ark:/88435/dsp015999n626m - - 1 - - Creative Commons Attribution 4.0 International - - - - Protein sequence space is vast; nature uses only an infinitesimal fraction - of possible sequences to sustain life. Are there solutions to biological - problems other than those provided by nature? Can we create artificial - proteins that sustain life? To investigate this question, the Hecht lab - has created combinatorial collections, or libraries, of novel sequences - with no homology to those found in living organisms. These libraries were - subjected to screens and selections, leading to the identification of - sequences with roles in catalysis, modulating gene regulation, and metal - homeostasis. However, the resulting functional proteins formed dynamic - rather than well-ordered structures. This impeded structural - characterization and made it difficult to ascertain a mechanism of action. - To address this, Christina Karas's thesis work focuses on developing - a new model of libraries based on the de novo protein S-824, a four-helix - bundle with a very stable three-dimensional structure. The first part of - this research focused on mutagenesis of S-824 and characterization of the - resulting proteins, revealing that this scaffold tolerates amino acid - substitutions, including buried polar residues and the removal of - hydrophobic side chains to create a putative cavity. Distinct from - previous libraries, Karas targeted variability to a specific region of the - protein, seeking to create a cavity and potential active site. The second - part of this work details the design and creation of a library encoding - 1.7 x 10^6 unique proteins, assembled from degenerate oligonucleotides. - The third and fourth parts of this work cover the screening effort for a - range of activities, both in vitro and in vivo. I found that this - collection binds heme readily, leading to abundant peroxidase activity. - Hits for lipase and phosphatase activity were also detected. This work - details the development of a new strategy for creating de novo sequences - geared toward function rather than structure. - - - \ No newline at end of file diff --git a/spec/system/data_migration/cklibrary_form_submission_spec.rb b/spec/system/data_migration/cklibrary_form_submission_spec.rb deleted file mode 100644 index 6cf421c25..000000000 --- a/spec/system/data_migration/cklibrary_form_submission_spec.rb +++ /dev/null @@ -1,73 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating cklibrary", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "CKavity Library: Next-Generation Sequencing" } - let(:alternative_title) { "A library of novel genes with combinatorially diverse cavities, built on a stably folded structural template" } - let(:description) do - "Protein sequence space is vast; nature uses only an infinitesimal fraction of possible sequences to sustain life. Are there solutions to biological problems other than those provided by nature? Can we create artificial proteins that sustain life? To investigate this question, the Hecht lab has created combinatorial collections, or libraries, of novel sequences with no homology to those found in living organisms. These libraries were subjected to screens and selections, leading to the identification of sequences with roles in catalysis, modulating gene regulation, and metal homeostasis. However, the resulting functional proteins formed dynamic rather than well-ordered structures. This impeded structural characterization and made it difficult to ascertain a mechanism of action. To address this, Christina Karas's thesis work focuses on developing a new model of libraries based on the de novo protein S-824, a four-helix bundle with a very stable three-dimensional structure. The first part of this research focused on mutagenesis of S-824 and characterization of the resulting proteins, revealing that this scaffold tolerates amino acid substitutions, including buried polar residues and the removal of hydrophobic side chains to create a putative cavity. Distinct from previous libraries, Karas targeted variability to a specific region of the protein, seeking to create a cavity and potential active site. The second part of this work details the design and creation of a library encoding 1.7 x 10^6 unique proteins, assembled from degenerate oligonucleotides. The third and fourth parts of this work cover the screening effort for a range of activities, both in vitro and in vivo. I found that this collection binds heme readily, leading to abundant peroxidase activity. Hits for lipase and phosphatase activity were also detected. This work details the development of a new strategy for creating de novo sequences geared toward function rather than structure." - end - let(:ark) { "ark:/88435/dsp015999n626m" } - let(:publisher) { "Princeton University" } - let(:doi) {} - let(:keywords) { "de novo genes, synthetic biology, Next-generation sequencing, DNA library" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/gg40-tc15") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - click_on "btn-add-title" - fill_in "new_title_1", with: alternative_title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Robert" - find("tr:last-child input[name='creators[][family_name]']").set "Leach" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Michael" - find("tr:last-child input[name='creators[][family_name]']").set "Hecht" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Christina" - find("tr:last-child input[name='creators[][family_name]']").set "Karas" - click_on "Additional Metadata" - fill_in "keywords", with: keywords - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2019 - select "Research Data", from: "group_id" - click_on "Curator Controlled" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - cklibrary_work = Work.last - expect(cklibrary_work.title).to eq title - expect(cklibrary_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(cklibrary_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/cklibrary.xml")) - export_spec_data("cklibrary.json", cklibrary_work.to_json) - end - end -end diff --git a/spec/system/data_migration/cytoskeletal.xml b/spec/system/data_migration/cytoskeletal.xml deleted file mode 100644 index 62c2d5e5d..000000000 --- a/spec/system/data_migration/cytoskeletal.xml +++ /dev/null @@ -1,117 +0,0 @@ - - 10.34770/r2dz-ys12 - - - Taylor, Jenny A - Jenny A - Taylor - - - Bratton, Benjamin P - Benjamin P - Bratton - - - Sichel, Sophie R - Sophie R - Sichel - - - Blair, Kris M - Kris M - Blair - - - Jacobs, Holly M - Holly M - Jacobs - - - DeMeester, Kristen E - Kristen E - DeMeester - - - Kuru, Erkin - Erkin - Kuru - - - Gray, Joe - Joe - Gray - - - Biboy, Jacob - Jacob - Biboy - - - VanNieuwenhze, Michael S - Michael S - VanNieuwenhze - - - Vollmer, Waldemar - Waldemar - Vollmer - - - Grimes, Catherine L - Catherine L - Grimes - - - Shaevitz, Joshua W - Joshua W - Shaevitz - - - Salama, Nina R - Nina R - Salama - - - - - Distinct cytoskeletal proteins define zones of enhanced cell wall - synthesis in Helicobacter pylori - - - Princeton University - - 2019 - - ark:/88435/dsp01h415pd457 - https://www.biorxiv.org/content/10.1101/545517v1 - https://doi.org/10.7554/eLife.52482 - - 1 - - Creative Commons Attribution 4.0 International - - - - Helical cell shape is necessary for efficient stomach colonization by - Helicobacter pylori, but the molecular mechanisms for generating helical - shape remain unclear. We show that the helical centerline pitch and radius - of wild-type H. pylori cells dictate surface curvatures of considerably - higher positive and negative Gaussian curvatures than those present in - straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of - short pulses with either N-acetylmuramic acid or D-alanine metabolic - probes showed that cell wall growth is enhanced at both sidewall curvature - extremes. Immunofluorescence revealed MreB is most abundant at negative - Gaussian curvature, while the bactofilin CcmA is most abundant at positive - Gaussian curvature. Strains expressing CcmA variants with altered - polymerization properties lose helical shape and associated positive - Gaussian curvatures. We thus propose a model where CcmA and MreB promote - PG synthesis at positive and negative Gaussian curvatures, respectively, - and that this patterning is one mechanism necessary for maintaining - helical shape. This dataset includes structured illumination fluorescence - microscopy images (SIM) and their associated cell shape reconstructions, - phase contrast micrographs, and transmission electron micrographs. See the - README.txt for detailed description of the strains and conditions - represented in each data file. - - - \ No newline at end of file diff --git a/spec/system/data_migration/cytoskeletal_form_submission_spec.rb b/spec/system/data_migration/cytoskeletal_form_submission_spec.rb deleted file mode 100644 index 1fdfd120a..000000000 --- a/spec/system/data_migration/cytoskeletal_form_submission_spec.rb +++ /dev/null @@ -1,133 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating cytoskeletal", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori" } - let(:description) do - "Helical cell shape is necessary for efficient stomach colonization by Helicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-type H. pylori cells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with either N-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape. This dataset includes structured illumination fluorescence microscopy images (SIM) and their associated cell shape reconstructions, phase contrast micrographs, and transmission electron micrographs. See the README.txt for detailed description of the strains and conditions represented in each data file." - end - let(:ark) { "ark:/88435/dsp01h415pd457" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/r2dz-ys12" } - let(:related_identifier) { "https://www.biorxiv.org/content/10.1101/545517v1" } - let(:related_identifier_type) { "arXiv" } - let(:relation_type) { "IsCitedBy" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/r2dz-ys12") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Jenny A" - find("tr:last-child input[name='creators[][family_name]']").set "Taylor" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Benjamin P" - find("tr:last-child input[name='creators[][family_name]']").set "Bratton" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Sophie R" - find("tr:last-child input[name='creators[][family_name]']").set "Sichel" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Kris M" - find("tr:last-child input[name='creators[][family_name]']").set "Blair" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Holly M" - find("tr:last-child input[name='creators[][family_name]']").set "Jacobs" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Kristen E" - find("tr:last-child input[name='creators[][family_name]']").set "DeMeester" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Erkin" - find("tr:last-child input[name='creators[][family_name]']").set "Kuru" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Joe" - find("tr:last-child input[name='creators[][family_name]']").set "Gray" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Jacob" - find("tr:last-child input[name='creators[][family_name]']").set "Biboy" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Michael S" - find("tr:last-child input[name='creators[][family_name]']").set "VanNieuwenhze" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Waldemar" - find("tr:last-child input[name='creators[][family_name]']").set "Vollmer" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Catherine L" - find("tr:last-child input[name='creators[][family_name]']").set "Grimes" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Joshua W" - find("tr:last-child input[name='creators[][family_name]']").set "Shaevitz" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Nina R" - find("tr:last-child input[name='creators[][family_name]']").set "Salama" - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2019 - select "Research Data", from: "group_id" - - # Select Additional Metadata Tab - click_on "Additional Metadata" - - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set related_identifier - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, related_identifier_type).select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - click_on "Add Another Related Object" - find("tr:last-child input[name='related_objects[][related_identifier]']").set "https://doi.org/10.7554/eLife.52482" - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, "DOI").select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - - # Select Curator Controlled Tab - click_on "Curator Controlled" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - cytoskeletal_work = Work.last - expect(cytoskeletal_work.title).to eq title - expect(cytoskeletal_work.ark).to eq ark - expect(cytoskeletal_work.resource.related_objects.first.related_identifier).to eq related_identifier - expect(cytoskeletal_work.resource.related_objects.first.related_identifier_type).to eq related_identifier_type - expect(cytoskeletal_work.resource.related_objects.first.relation_type).to eq relation_type - # ARK is not a related object in the resource, but it IS a "related identifer" in the DataCite serialization - # This object has 2 related objects, but 3 related identifiers - expect(cytoskeletal_work.resource.related_objects.count).to eq 2 - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(cytoskeletal_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/cytoskeletal.xml")) - export_spec_data("cytoskeletal.json", cytoskeletal_work.to_json) - end - end -end diff --git a/spec/system/data_migration/design_arrangment.xml b/spec/system/data_migration/design_arrangment.xml deleted file mode 100644 index a5393425d..000000000 --- a/spec/system/data_migration/design_arrangment.xml +++ /dev/null @@ -1,95 +0,0 @@ - - 10.11578/1888258 - - - Hammond, Kenneth - Kenneth - Hammond - 0000-0002-1104-4434 - - - Zhu, Caoxiang - Caoxiang - Zhu - 0000-0003-2337-3232 - - - Corrigan, Keith - Keith - Corrigan - 0000-0001-9857-451X - - - Gates, David - David - Gates - 0000-0001-5679-3124 - - - Lown, Robert - Robert - Lown - - - Mercurio, Robert - Robert - Mercurio - - - Qian, Tony - Tony - Qian - 0000-0002-6536-5399 - - - Zarnstorff, Michael - Michael - Zarnstorff - 0000-0001-7525-0539 - - - - - Design of an arrangement of cubic magnets for a quasi-axisymmetric - stellarator experiment - - - Princeton University - - 2022 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - - ark:/88435/dsp01x059cb547 - https://doi.org/10.1088/1741-4326/ac906e - - 1 - - Creative Commons Attribution 4.0 International - - - - The usage of permanent magnets to shape the confining field of a - stellarator has the potential to reduce or eliminate the need for - non-planar coils. As a proof-of-concept for this idea, we have developed a - procedure for designing an array of cubic permanent magnets that works in - tandem with a set of toroidal-field coils to confine a stellarator plasma. - All of the magnets in the design are constrained to have identical - geometry and one of three polarization types in order to simplify - fabrication while still producing sufficient field accuracy. We present - some of the key steps leading to the design, including the geometric - arrangement of the magnets around the device, the procedure for optimizing - the polarizations according to three allowable magnet types, and the - choice of magnet types to be used. We apply these methods to design an - array of rare-Earth permanent magnets that can be paired with a set of - planar toroidal-field coils to confine a quasi-axisymmetric plasma with a - toroidal magnetic field strength of about 0.5 T on axis. Consult the file - README.txt for a more detailed description of the contents. - - - \ No newline at end of file diff --git a/spec/system/data_migration/design_arrangment_form_submission_spec.rb b/spec/system/data_migration/design_arrangment_form_submission_spec.rb deleted file mode 100644 index 07f527a1e..000000000 --- a/spec/system/data_migration/design_arrangment_form_submission_spec.rb +++ /dev/null @@ -1,109 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating design-arrangment", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "Design of an arrangement of cubic magnets for a quasi-axisymmetric stellarator experiment" } - let(:description) do - "The usage of permanent magnets to shape the confining field of a stellarator has the potential to reduce or eliminate the need for non-planar coils. As a proof-of-concept for this idea, we have developed a procedure for designing an array of cubic permanent magnets that works in tandem with a set of toroidal-field coils to confine a stellarator plasma. All of the magnets in the design are constrained to have identical geometry and one of three polarization types in order to simplify fabrication while still producing sufficient field accuracy. We present some of the key steps leading to the design, including the geometric arrangement of the magnets around the device, the procedure for optimizing the polarizations according to three allowable magnet types, and the choice of magnet types to be used. We apply these methods to design an array of rare-Earth permanent magnets that can be paired with a set of planar toroidal-field coils to confine a quasi-axisymmetric plasma with a toroidal magnetic field strength of about 0.5 T on axis. - -Consult the file README.txt for a more detailed description of the contents." - end - let(:ark) { "ark:/88435/dsp01x059cb547" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.11578/1888258" } - let(:keywords) { "" } - let(:relation_type) { "IsCitedBy" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.11578")) - stub_request(:get, "https://handle.stage.datacite.org/10.11578/1888258") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PPPL Dataset") - click_on "Migrate PPPL Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-1104-4434" - find("tr:last-child input[name='creators[][given_name]']").set "Kenneth" - find("tr:last-child input[name='creators[][family_name]']").set "Hammond" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-2337-3232" - find("tr:last-child input[name='creators[][given_name]']").set "Caoxiang" - find("tr:last-child input[name='creators[][family_name]']").set "Zhu" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-9857-451X" - find("tr:last-child input[name='creators[][given_name]']").set "Keith" - find("tr:last-child input[name='creators[][family_name]']").set "Corrigan" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-5679-3124" - find("tr:last-child input[name='creators[][given_name]']").set "David" - find("tr:last-child input[name='creators[][family_name]']").set "Gates" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Robert" - find("tr:last-child input[name='creators[][family_name]']").set "Lown" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Robert" - find("tr:last-child input[name='creators[][family_name]']").set "Mercurio" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-6536-5399" - find("tr:last-child input[name='creators[][given_name]']").set "Tony" - find("tr:last-child input[name='creators[][family_name]']").set "Qian" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-7525-0539" - find("tr:last-child input[name='creators[][given_name]']").set "Michael" - find("tr:last-child input[name='creators[][family_name]']").set "Zarnstorff" - - click_on "Additional Metadata" - expect(page).to have_content "Applied Materials and Sustainability Sciences" - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set "https://doi.org/10.1088/1741-4326/ac906e" - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, "DOI").select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2022 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Plasma Physics Lab (PPPL)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - design_arrangment_work = Work.last - expect(design_arrangment_work.title).to eq title - expect(design_arrangment_work.ark).to eq ark - - # Check that RORs were persisted as funder names - funders = design_arrangment_work.resource.funders.map(&:funder_name).uniq - expect(funders).to contain_exactly("United States Department of Energy") - - # # Ensure the datacite record produced validates against our local copy of the datacite schema. - # # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(design_arrangment_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/design_arrangment.xml")) - export_spec_data("design_arrangment.json", design_arrangment_work.to_json) - end - end -end diff --git a/spec/system/data_migration/dynamic_tension.xml b/spec/system/data_migration/dynamic_tension.xml deleted file mode 100644 index 1c35a8a46..000000000 --- a/spec/system/data_migration/dynamic_tension.xml +++ /dev/null @@ -1,96 +0,0 @@ - - 10.11578/1366453 - - - Myers, Clayton - Clayton - Myers - 0000-0003-4539-8406 - - - Yamada, Maasaki - Maasaki - Yamada - 0000-0003-4996-1649 - - - Ji, Hantao - Hantao - Ji - 0000-0001-9600-9963 - - - Yoo, Jongsoo - Jongsoo - Yoo - 0000-0003-3881-1995 - - - Fox, William - William - Fox - 0000-0001-6289-858X - - - Jara-Almonte, Jonathan - Jonathan - Jara-Almonte - 0000-0003-0760-6198 - - - Savcheva, Antonia - Antonia - Savcheva - - - DeLuca, Edward E - Edward E - DeLuca - - - - A dynamic magnetic tension force as the cause of failed solar eruptions - - Princeton University - - 2015 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - - ark:/88435/dsp01j3860933c - - 1 - - Creative Commons Attribution 4.0 International - - - - Coronal mass ejections are solar eruptions driven by a sudden release of - magnetic energy stored in the Sun's corona. In many cases, this - magnetic energy is stored in long-lived, arched structures called magnetic - flux ropes. When a flux rope destabilizes, it can either erupt and produce - a coronal mass ejection or fail and collapse back towards the Sun. The - prevailing belief is that the outcome of a given event is determined by a - magnetohydrodynamic force imbalance called the torus instability. This - belief is challenged, however, by observations indicating that - torus-unstable flux ropes sometimes fail to erupt. This contradiction has - not yet been resolved because of a lack of coronal magnetic field - measurements and the limitations of idealized numerical modelling. Here we - report the results of a laboratory experiment that reveal a previously - unknown eruption criterion below which torus-unstable flux ropes fail to - erupt. We find that such 'failed torus' events occur when the - guide magnetic field (that is, the ambient field that runs toroidally - along the flux rope) is strong enough to prevent the flux rope from - kinking. Under these conditions, the guide field interacts with electric - currents in the flux rope to produce a dynamic toroidal field tension - force that halts the eruption. This magnetic tension force is missing from - existing eruption models, which is why such models cannot explain or - predict failed torus events. - - - \ No newline at end of file diff --git a/spec/system/data_migration/dynamic_tension_form_submission_spec.rb b/spec/system/data_migration/dynamic_tension_form_submission_spec.rb deleted file mode 100644 index a64174aa0..000000000 --- a/spec/system/data_migration/dynamic_tension_form_submission_spec.rb +++ /dev/null @@ -1,102 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating dynamic-tension", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "A dynamic magnetic tension force as the cause of failed solar eruptions" } - let(:description) do - "Coronal mass ejections are solar eruptions driven by a sudden release of magnetic energy stored in the Sun's corona. In many cases, this magnetic energy is stored in long-lived, arched structures called magnetic flux ropes. When a flux rope destabilizes, it can either erupt and produce a coronal mass ejection or fail and collapse back towards the Sun. The prevailing belief is that the outcome of a given event is determined by a magnetohydrodynamic force imbalance called the torus instability. This belief is challenged, however, by observations indicating that torus-unstable flux ropes sometimes fail to erupt. This contradiction has not yet been resolved because of a lack of coronal magnetic field measurements and the limitations of idealized numerical modelling. Here we report the results of a laboratory experiment that reveal a previously unknown eruption criterion below which torus-unstable flux ropes fail to erupt. We find that such 'failed torus' events occur when the guide magnetic field (that is, the ambient field that runs toroidally along the flux rope) is strong enough to prevent the flux rope from kinking. Under these conditions, the guide field interacts with electric currents in the flux rope to produce a dynamic toroidal field tension force that halts the eruption. This magnetic tension force is missing from existing eruption models, which is why such models cannot explain or predict failed torus events." - end - let(:ark) { "ark:/88435/dsp01j3860933c" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.11578/1366453" } - let(:keywords) { "laboratory plasma astrophysics, solar eruptions, coronal mass ejections, magnetohydrodynamic instabilities" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.11578")) - stub_request(:get, "https://handle.stage.datacite.org/10.11578/1366453") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PPPL Dataset") - click_on "Migrate PPPL Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-4539-8406" - find("tr:last-child input[name='creators[][given_name]']").set "Clayton" - find("tr:last-child input[name='creators[][family_name]']").set "Myers" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-4996-1649" - find("tr:last-child input[name='creators[][given_name]']").set "Maasaki" - find("tr:last-child input[name='creators[][family_name]']").set "Yamada" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-9600-9963" - find("tr:last-child input[name='creators[][given_name]']").set "Hantao" - find("tr:last-child input[name='creators[][family_name]']").set "Ji" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-3881-1995" - find("tr:last-child input[name='creators[][given_name]']").set "Jongsoo" - find("tr:last-child input[name='creators[][family_name]']").set "Yoo" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-6289-858X" - find("tr:last-child input[name='creators[][given_name]']").set "William" - find("tr:last-child input[name='creators[][family_name]']").set "Fox" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-0760-6198" - find("tr:last-child input[name='creators[][given_name]']").set "Jonathan" - find("tr:last-child input[name='creators[][family_name]']").set "Jara-Almonte" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Antonia" - find("tr:last-child input[name='creators[][family_name]']").set "Savcheva" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Edward E" - find("tr:last-child input[name='creators[][family_name]']").set "DeLuca" - - click_on "Additional Metadata" - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2015 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Plasma Physics Lab (PPPL)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - dynamic_tension_work = Work.last - expect(dynamic_tension_work.title).to eq title - expect(dynamic_tension_work.ark).to eq ark - - # Check that RORs were persisted as funder names - funders = dynamic_tension_work.resource.funders.map(&:funder_name).uniq - expect(funders).to contain_exactly("United States Department of Energy") - - # # Ensure the datacite record produced validates against our local copy of the datacite schema. - # # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(dynamic_tension_work) - expect(datacite.valid?).to eq true - - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/dynamic_tension.xml")) - export_spec_data("dynamic_tension.json", dynamic_tension_work.to_json) - end - end -end diff --git a/spec/system/data_migration/electromagnetic.xml b/spec/system/data_migration/electromagnetic.xml deleted file mode 100644 index 0ba0830fc..000000000 --- a/spec/system/data_migration/electromagnetic.xml +++ /dev/null @@ -1,103 +0,0 @@ - - 10.1063/5.0097855 - - - Hager, Robert - Robert - Hager - 0000-0002-4624-3150 - - - Ku, Seung-Hoe - Seung-Hoe - Ku - 0000-0002-9964-1208 - - - Sharma, Ami Y. - Ami Y. - Sharma - 0000-0002-7946-7425 - - - Churchill, Randy Michael - Randy Michael - Churchill - 0000-0001-5711-746X - - - Chang, C.S. - C.S. - Chang - 0000-0002-3346-5731 - - - Scheinberg, Aaron - Aaron - Scheinberg - - - - - Electromagnetic total-f algorithm for gyrokinetic particle-in-cell - simulations of boundary plasma in XGC - - - Princeton University - - 2022 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC05-00OR22725 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-06CH11357 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-05CH11231 - - - - ark:/88435/dsp01zw12z8539 - https://doi.org/10.1063/5.0097855 - - 1 - - Creative Commons Attribution 4.0 International - - - - The simplified delta-f mixed-variable/pull-back electromagnetic simulation - algorithm implemented in XGC for core plasma simulations by Cole et al. - [Phys. Plasmas 28, 034501 (2021)] has been generalized to a total-f - electromagnetic algorithm that can include, for the first time, the - boundary plasma in diverted magnetic geometry with neutral particle - recycling, turbulence and neoclassical physics. The delta-f - mixed-variable/pull-back electromagnetic implementation is based on the - pioneering work by Kleiber and Mischenko et al. [Kleiber et al., Phys. - Plasmas 23, 032501 (2016); Mishchenko et al., Comput. Phys. Commun. 238, - 194 (2019)]. An electromagnetic demonstration simulation is performed in a - DIII-D-like, H-mode boundary plasma, including a corresponding comparative - electrostatic simulation, which confirms that the electromagnetic - simulation is necessary for a higher fidelity understanding of the - electron particle and heat transport even at the low-beta pedestal foot in - the vicinity of the magnetic separatrix.. This data set includes the data - visualized in figures 2-7 in Electromagnetic total-f algorithm for - gyrokinetic particle-in-cell simulations of boundary plasma in XGC Physics - of Plasmas 29, 112308 (2022); https://doi.org/10.1063/5.0097855. The file - names indicate to which figure the data belongs. The data files themselves - are in self-descriptive HDF5 format. - - - \ No newline at end of file diff --git a/spec/system/data_migration/electromagnetic_form_submission_spec.rb b/spec/system/data_migration/electromagnetic_form_submission_spec.rb deleted file mode 100644 index 8204fc01b..000000000 --- a/spec/system/data_migration/electromagnetic_form_submission_spec.rb +++ /dev/null @@ -1,105 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for electromagnetic", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "Electromagnetic total-f algorithm for gyrokinetic particle-in-cell simulations of boundary plasma in XGC" } - let(:description) do - "The simplified delta-f mixed-variable/pull-back electromagnetic simulation algorithm implemented in XGC for core plasma simulations by Cole et al. [Phys. Plasmas 28, 034501 (2021)] has been generalized to a total-f electromagnetic algorithm that can include, for the first time, the boundary plasma in diverted magnetic geometry with neutral particle recycling, turbulence and neoclassical physics. The delta-f mixed-variable/pull-back electromagnetic implementation is based on the pioneering work by Kleiber and Mischenko et al. [Kleiber et al., Phys. Plasmas 23, 032501 (2016); Mishchenko et al., Comput. Phys. Commun. 238, 194 (2019)]. An electromagnetic demonstration simulation is performed in a DIII-D-like, H-mode boundary plasma, including a corresponding comparative electrostatic simulation, which confirms that the electromagnetic simulation is necessary for a higher fidelity understanding of the electron particle and heat transport even at the low-beta pedestal foot in the vicinity of the magnetic separatrix.. - -This data set includes the data visualized in figures 2-7 in Electromagnetic total-f algorithm for gyrokinetic particle-in-cell simulations of boundary plasma in XGC Physics of Plasmas 29, 112308 (2022); https://doi.org/10.1063/5.0097855. The file names indicate to which figure the data belongs. The data files themselves are in self-descriptive HDF5 format." - end - let(:ark) { "ark:/88435/dsp01zw12z8539" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.1063/5.0097855" } - let(:keywords) { "Tokamak, Magnetic confinement fusion, gyrokinetic, XGC" } - let(:relation_type) { "IsCitedBy" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.1063")) - stub_request(:get, "https://handle.stage.datacite.org/10.1063/5.0097855") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PPPL Dataset") - click_on "Migrate PPPL Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-4624-3150" - find("tr:last-child input[name='creators[][given_name]']").set "Robert" - find("tr:last-child input[name='creators[][family_name]']").set "Hager" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-9964-1208" - find("tr:last-child input[name='creators[][given_name]']").set "Seung-Hoe" - find("tr:last-child input[name='creators[][family_name]']").set "Ku" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-7946-7425" - find("tr:last-child input[name='creators[][given_name]']").set "Ami Y." - find("tr:last-child input[name='creators[][family_name]']").set "Sharma" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-5711-746X" - find("tr:last-child input[name='creators[][given_name]']").set "Randy Michael" - find("tr:last-child input[name='creators[][family_name]']").set "Churchill" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-3346-5731" - find("tr:last-child input[name='creators[][given_name]']").set "C.S." - find("tr:last-child input[name='creators[][family_name]']").set "Chang" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Aaron" - find("tr:last-child input[name='creators[][family_name]']").set "Scheinberg" - - click_on "Additional Metadata" - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][award_number]']").set "DE-AC05-00OR22725" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][award_number]']").set "DE-AC02-06CH11357" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][award_number]']").set "DE-AC02-05CH11231" - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set "https://doi.org/10.1063/5.0097855" - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, "DOI").select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2022 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Plasma Physics Lab (PPPL)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - electromagnetic_work = Work.last - expect(electromagnetic_work.title).to eq title - expect(electromagnetic_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(electromagnetic_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/electromagnetic.xml")) - export_spec_data("electromagnetic.json", electromagnetic_work.to_json) - end - end -end diff --git a/spec/system/data_migration/femtosecond.xml b/spec/system/data_migration/femtosecond.xml deleted file mode 100644 index b8ee81d82..000000000 --- a/spec/system/data_migration/femtosecond.xml +++ /dev/null @@ -1,180 +0,0 @@ - - 10.34770/gg40-tc15 - - - Kim, Donghoon - Donghoon - Kim - - - Tracy, Sally J - Sally J - Tracy - - - Smith, Raymond F - Raymond F - Smith - - - Gleason, Arianna E - Arianna E - Gleason - - - Bolme, Cindy A - Cindy A - Bolme - - - Prakapenka, Vitali B - Vitali B - Prakapenka - - - Appel, Karen - Karen - Appel - - - Speziable, Sergio - Sergio - Speziable - - - Wicks, June K - June K - Wicks - - - Berryman, Eleanor J - Eleanor J - Berryman - - - Han, Sirus K - Sirus K - Han - - - Schoelmerich, Markus O - Markus O - Schoelmerich - - - Lee, Hae Ja - Hae Ja - Lee - - - Nagler, Bob - Bob - Nagler - - - Cunningham, Eric F - Eric F - Cunningham - - - Akin, Minta C - Minta C - Akin - - - Asimow, Paul D - Paul D - Asimow - - - Eggert, Jon H - Jon H - Eggert - - - Duffy, Thomas S - Thomas S - Duffy - - - - Femtosecond X-ray Diffraction of Laser-shocked Forsterite (Mg2SiO4) to 122 GPa - - Princeton University - - 2020 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-SC0018925 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-76SF00515 - - - National Science Foundation - https://ror.org/021nxhr62 - EAR-1644614 - - - National Science Foundation - https://ror.org/021nxhr62 - EAR-1446969 - - - National Science Foundation - https://ror.org/021nxhr62 - EAR-1725349 - - - Deutsche Forschungsgemeinschaft - https://ror.org/018mejw64 - AP 262/2-1 - - - Deutsche Forschungsgemeinschaft - https://ror.org/018mejw64 - FOR2440 - - - - ark:/88435/dsp01rj4307478 - - 1 - - Creative Commons Attribution 4.0 International - - - - The behavior of forsterite, Mg2SiO4, under dynamic compression is of - fundamental importance for understanding its phase transformations and - high-pressure behavior. Here, we have carried out an in situ X-ray - diffraction study of laser-shocked poly- and single-crystal forsterite - (a-, b-, and c- orientations) from 19 to 122 GPa using the Matter in - Extreme Conditions end-station of the Linac Coherent Light Source. Under - laser-based shock loading, forsterite does not transform to the - high-pressure equilibrium assemblage of MgSiO3 bridgmanite and MgO - periclase, as was suggested previously. Instead, we observe forsterite and - forsterite III, a metastable polymorph of Mg2SiO4, coexisting in a - mixed-phase region from 33 to 75 GPa for both polycrystalline and - single-crystal samples. Densities inferred from X-ray diffraction data are - consistent with earlier gas-gun shock data. At higher stress, the behavior - observed is sample-dependent. Polycrystalline samples undergo - amorphization above 79 GPa. For [010]- and [001]-oriented crystals, a - mixture of crystalline and amorphous material is observed to 108 GPa, - whereas the [100]-oriented crystal adopts an unknown crystal structure at - 122 GPa. The Q values of the first two sharp diffraction peaks of - amorphous Mg2SiO4 show a similar trend with compression as those observed - for MgSiO3 glass in both recent static and laser-compression experiments. - Upon release to ambient pressure, all samples retain or revert to - forsterite with evidence for amorphous material also present in some - cases. This study demonstrates the utility of femtosecond free-electron - laser X-ray sources for probing the time evolution of high-pressure - silicates through the nanosecond-scale events of shock compression and - release. - - - \ No newline at end of file diff --git a/spec/system/data_migration/femtosecond_form_submission_spec.rb b/spec/system/data_migration/femtosecond_form_submission_spec.rb deleted file mode 100644 index ef27cf97c..000000000 --- a/spec/system/data_migration/femtosecond_form_submission_spec.rb +++ /dev/null @@ -1,163 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating femtosecond", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "Femtosecond X-ray Diffraction of Laser-shocked Forsterite (Mg2SiO4) to 122 GPa" } - let(:description) do - "The behavior of forsterite, Mg2SiO4, under dynamic compression is of fundamental importance for understanding its phase transformations and high-pressure behavior. Here, we have carried out an in situ X-ray diffraction study of laser-shocked poly- and single-crystal forsterite (a-, b-, and c- orientations) from 19 to 122 GPa using the Matter in Extreme Conditions end-station of the Linac Coherent Light Source. Under laser-based shock loading, forsterite does not transform to the high-pressure equilibrium assemblage of MgSiO3 bridgmanite and MgO periclase, as was suggested previously. Instead, we observe forsterite and forsterite III, a metastable polymorph of Mg2SiO4, coexisting in a mixed-phase region from 33 to 75 GPa for both polycrystalline and single-crystal samples. Densities inferred from X-ray diffraction data are consistent with earlier gas-gun shock data. At higher stress, the behavior observed is sample-dependent. Polycrystalline samples undergo amorphization above 79 GPa. For [010]- and [001]-oriented crystals, a mixture of crystalline and amorphous material is observed to 108 GPa, whereas the [100]-oriented crystal adopts an unknown crystal structure at 122 GPa. The Q values of the first two sharp diffraction peaks of amorphous Mg2SiO4 show a similar trend with compression as those observed for MgSiO3 glass in both recent static and laser-compression experiments. Upon release to ambient pressure, all samples retain or revert to forsterite with evidence for amorphous material also present in some cases. This study demonstrates the utility of femtosecond free-electron laser X-ray sources for probing the time evolution of high-pressure silicates through the nanosecond-scale events of shock compression and release." - end - let(:ark) { "ark:/88435/dsp01rj4307478" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/gg40-tc15" } - let(:keywords) { "shock compression, forsterite, phase transition, amorphization" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/gg40-tc15") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Donghoon" - find("tr:last-child input[name='creators[][family_name]']").set "Kim" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Sally J" - find("tr:last-child input[name='creators[][family_name]']").set "Tracy" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Raymond F" - find("tr:last-child input[name='creators[][family_name]']").set "Smith" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Arianna E" - find("tr:last-child input[name='creators[][family_name]']").set "Gleason" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Cindy A" - find("tr:last-child input[name='creators[][family_name]']").set "Bolme" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Vitali B" - find("tr:last-child input[name='creators[][family_name]']").set "Prakapenka" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Karen" - find("tr:last-child input[name='creators[][family_name]']").set "Appel" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Sergio" - find("tr:last-child input[name='creators[][family_name]']").set "Speziable" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "June K" - find("tr:last-child input[name='creators[][family_name]']").set "Wicks" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Eleanor J" - find("tr:last-child input[name='creators[][family_name]']").set "Berryman" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Sirus K" - find("tr:last-child input[name='creators[][family_name]']").set "Han" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Markus O" - find("tr:last-child input[name='creators[][family_name]']").set "Schoelmerich" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Hae Ja" - find("tr:last-child input[name='creators[][family_name]']").set "Lee" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Bob" - find("tr:last-child input[name='creators[][family_name]']").set "Nagler" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Eric F" - find("tr:last-child input[name='creators[][family_name]']").set "Cunningham" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Minta C" - find("tr:last-child input[name='creators[][family_name]']").set "Akin" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Paul D" - find("tr:last-child input[name='creators[][family_name]']").set "Asimow" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Jon H" - find("tr:last-child input[name='creators[][family_name]']").set "Eggert" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Thomas S" - find("tr:last-child input[name='creators[][family_name]']").set "Duffy" - - click_on "Additional Metadata" - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-SC0018925" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][award_number]']").set "DE-AC02-76SF00515" - click_on "Add Another Funder" - # https://ror.org/021nxhr62 == ROR for National Science Foundation - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][ror]']").set "https://ror.org/021nxhr62" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][award_number]']").set "EAR-1644614" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][ror]']").set "https://ror.org/021nxhr62" - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][award_number]']").set "EAR-1446969" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[5]//input[@name='funders[][ror]']").set "https://ror.org/021nxhr62" - page.find(:xpath, "//table[@id='funding']//tr[5]//input[@name='funders[][award_number]']").set "EAR-1725349" - click_on "Add Another Funder" - # https://ror.org/018mejw64 == ROR for Deutsche Forschungsgemeinschaft a.k.a. DFG, German Research Foundation - page.find(:xpath, "//table[@id='funding']//tr[6]//input[@name='funders[][ror]']").set "https://ror.org/018mejw64" - page.find(:xpath, "//table[@id='funding']//tr[6]//input[@name='funders[][award_number]']").set "AP 262/2-1" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[7]//input[@name='funders[][ror]']").set "https://ror.org/018mejw64" - page.find(:xpath, "//table[@id='funding']//tr[7]//input[@name='funders[][award_number]']").set "FOR2440" - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2020 - select "Research Data", from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - femtosecond_work = Work.last - expect(femtosecond_work.title).to eq title - expect(femtosecond_work.ark).to eq ark - - # Check that RORs were persisted as funder names - funders = femtosecond_work.resource.funders.map(&:funder_name).uniq - expect(funders).to contain_exactly("United States Department of Energy", "National Science Foundation", "Deutsche Forschungsgemeinschaft") - - # # Ensure the datacite record produced validates against our local copy of the datacite schema. - # # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(femtosecond_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/femtosecond.xml")) - export_spec_data("femtosecond.json", femtosecond_work.to_json) - end - end -end diff --git a/spec/system/data_migration/flume.xml b/spec/system/data_migration/flume.xml deleted file mode 100644 index bc7f441d3..000000000 --- a/spec/system/data_migration/flume.xml +++ /dev/null @@ -1,60 +0,0 @@ - - 10.34770/7hyr-rf67 - - - Ghannam, Khaled - Khaled - Ghannam - - - Poggi, Davide - Davide - Poggi - - - Katul, Gabriel - Gabriel - Katul - - - Bou-Zeid, Elie - Elie - Bou-Zeid - - - - - Data from a flume experiment of passive scalar diffusion within vegetation - canopies using laser-induced fluorescence - - - Princeton University - - 2020 - - ark:/88435/dsp01qj72pb044 - - 1 - - Creative Commons Attribution 4.0 International - - - - This dataset is a sequence of laser-induced fluorescence images of a dye - injected in a channel flow with canopy-like stainless steel rods - simulating a vegetation canopy stand. The data is acquired close to the - channel bottom at z/h=0.2, where z is the height referenced to the channel - bed and h is the canopy height. The dataset provides spatial distribution - of scalar concentration in a plane parallel to the channel bed. The data - has been used (but the data itself has not been published or available to - the public) in previous work. The references are: Ghannam, K., Poggi, D., - Porporato, A., & Katul, G. (2015). The spatio-temporal statistical - structure and ergodic behaviour of scalar turbulence within a rod canopy. - Boundary-Layer Meteorology,157(3), 447–460. Ghannam, K, Poggi, D., - Bou-Zeid, E., Katul, G. (2020). Inverse cascade evidenced by information - entropy of passive scalars in submerged canopy flows. Geophysical Research - Letters (accepted). The attached readme.txt file explains the data - attributes - - - \ No newline at end of file diff --git a/spec/system/data_migration/flume_form_submission_spec.rb b/spec/system/data_migration/flume_form_submission_spec.rb deleted file mode 100644 index 35ca8ca12..000000000 --- a/spec/system/data_migration/flume_form_submission_spec.rb +++ /dev/null @@ -1,75 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating flume", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "Data from a flume experiment of passive scalar diffusion within vegetation canopies using laser-induced fluorescence" } - let(:description) do - "This dataset is a sequence of laser-induced fluorescence images of a dye injected in a channel flow with canopy-like stainless steel rods simulating a vegetation canopy stand. The data is acquired close to the channel bottom at z/h=0.2, where z is the height referenced to the channel bed and h is the canopy height. The dataset provides spatial distribution of scalar concentration in a plane parallel to the channel bed. The data has been used (but the data itself has not been published or available to the public) in previous work. The references are: Ghannam, K., Poggi, D., Porporato, A., & Katul, G. (2015). The spatio-temporal statistical structure and ergodic behaviour of scalar turbulence within a rod canopy. Boundary-Layer Meteorology,157(3), 447–460. Ghannam, K, Poggi, D., Bou-Zeid, E., Katul, G. (2020). Inverse cascade evidenced by information entropy of passive scalars in submerged canopy flows. Geophysical Research Letters (accepted). - -The attached readme.txt file explains the data attributes" - end - let(:ark) { "ark:/88435/dsp01qj72pb044" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/7hyr-rf67" } - let(:keywords) { "vegetation canopy turbulence, flume experiments, scalar diffusion, land-atmosphere interactions" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/7hyr-rf67") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/" - click_on(user.uid) - expect(page).to have_link("Migrate PRDS Dataset") - click_on "Migrate PRDS Dataset" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Khaled" - find("tr:last-child input[name='creators[][family_name]']").set "Ghannam" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Davide" - find("tr:last-child input[name='creators[][family_name]']").set "Poggi" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Gabriel" - find("tr:last-child input[name='creators[][family_name]']").set "Katul" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Elie" - find("tr:last-child input[name='creators[][family_name]']").set "Bou-Zeid" - click_on "Additional Metadata" - fill_in "keywords", with: keywords - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2020 - fill_in "doi", with: doi - fill_in "ark", with: ark - select "Research Data", from: "group_id" - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - expect(page).to have_content "Princeton Research Data Service (PRDS)" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - flume_work = Work.last - expect(flume_work.title).to eq title - expect(flume_work.ark).to eq ark - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(flume_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/flume.xml")) - export_spec_data("flume.json", flume_work.to_json) - end - end -end diff --git a/spec/system/data_migration/fusion_energy.xml b/spec/system/data_migration/fusion_energy.xml deleted file mode 100644 index 27c9e4ba4..000000000 --- a/spec/system/data_migration/fusion_energy.xml +++ /dev/null @@ -1,69 +0,0 @@ - - 10.34770/f8em-3c49 - - - Schwartz, Jacob A. - Jacob A. - Schwartz - 0000-0001-9636-8181 - - - Ricks, Wilson - Wilson - Ricks - - - Kolemen, Egemen - Egemen - Kolemen - 0000-0003-4212-3247 - - - Jenkins, Jesse D. - Jesse D. - Jenkins - 0000-0002-9670-7793 - - - - - Data for "The value of fusion energy to a decarbonized United States - electric grid" - - - Princeton University - - 2022 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - - ark:/88435/dsp012j62s808w - - 1 - - Creative Commons Attribution 4.0 International - - - - Fusion could be a part of future decarbonized electricity systems, but it - will need to compete with other technologies. In particular, pulsed - tokamaks plants have a unique operational mode, and evaluating which - characteristics make them economically competitive can help select between - design pathways. Using a capacity expansion and operations model, we - determined cost thresholds for pulsed tokamaks to reach a range of - penetration levels in a future decarbonized US Eastern Interconnection. - The required capital cost to reach a fusion capacity of 100 GW varied from - $3000 to $7200/kW, and the equilibrium penetration increases rapidly with - decreasing cost. The value per unit power capacity depends on the variable - operational cost and on cost of its competition, particularly fission, - much more than on the pulse cycle parameters. These findings can therefore - provide initial cost targets for fusion more generally in the United - States. - - - \ No newline at end of file diff --git a/spec/system/data_migration/fusion_energy_form_submission_spec.rb b/spec/system/data_migration/fusion_energy_form_submission_spec.rb deleted file mode 100644 index 005865796..000000000 --- a/spec/system/data_migration/fusion_energy_form_submission_spec.rb +++ /dev/null @@ -1,85 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating fusion energy", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { 'Data for "The value of fusion energy to a decarbonized United States electric grid"' } - let(:description) do - "Fusion could be a part of future decarbonized electricity systems, but it will need to compete with other technologies. In particular, pulsed tokamaks plants have a unique operational mode, and evaluating which characteristics make them economically competitive can help select between design pathways. Using a capacity expansion and operations model, we determined cost thresholds for pulsed tokamaks to reach a range of penetration levels in a future decarbonized US Eastern Interconnection. The required capital cost to reach a fusion capacity of 100 GW varied from $3000 to $7200/kW, and the equilibrium penetration increases rapidly with decreasing cost. The value per unit power capacity depends on the variable operational cost and on cost of its competition, particularly fission, much more than on the pulse cycle parameters. These findings can therefore provide initial cost targets for fusion more generally in the United States." - end - let(:ark) { "ark:/88435/dsp012j62s808w" } - let(:collection_tags) { ["Discovery Plasma Science"] } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/f8em-3c49" } - let(:keywords) { "fusion, economics, cost, value, tokamak, power plant" } - - before do - stub_request(:get, "https://handle.stage.datacite.org/10.34770/f8em-3c49") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/works/new?migrate=true" - - ## Required Metadata Tab - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-9636-8181" - find("tr:last-child input[name='creators[][given_name]']").set "Jacob A." - find("tr:last-child input[name='creators[][family_name]']").set "Schwartz" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Wilson" - find("tr:last-child input[name='creators[][family_name]']").set "Ricks" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-4212-3247" - find("tr:last-child input[name='creators[][given_name]']").set "Egemen" - find("tr:last-child input[name='creators[][family_name]']").set "Kolemen" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-9670-7793" - find("tr:last-child input[name='creators[][given_name]']").set "Jesse D." - find("tr:last-child input[name='creators[][family_name]']").set "Jenkins" - - ## Additional Metadata Tab - click_on "Additional Metadata" - - # Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - - select "Natural Sciences", from: "domains" - select "Princeton Plasma Physics Laboratory", from: "communities" - select "Discovery Plasma Science", from: "subcommunities" - - ## Curator Controlled Tab - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2022 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - fill_in "collection_tags", with: collection_tags.join(", ") - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - fusion_energy_work = Work.last - expect(fusion_energy_work.title).to eq title - expect(fusion_energy_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(fusion_energy_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/fusion_energy.xml")) - export_spec_data("fusion_energy.json", fusion_energy_work.to_json) - end - end -end diff --git a/spec/system/data_migration/hybrid_drift.xml b/spec/system/data_migration/hybrid_drift.xml deleted file mode 100644 index dd6e67752..000000000 --- a/spec/system/data_migration/hybrid_drift.xml +++ /dev/null @@ -1,143 +0,0 @@ - - 10.11578/1814938 - - - Yoo, Jongsoo - Jongsoo - Yoo - 0000-0003-3881-1995 - - - Jeong-Young, Ji - Ji - Jeong-Young - - - M.V., Ambat - Ambat - M.V. - - - Shan, Wang - Wang - Shan - - - Hantao, Ji - Ji - Hantao - 0000-0001-9600-9963 - - - Jenson, Lo - Lo - Jenson - - - Bowen, Li - Li - Bowen - - - Yang, Ren - Ren - Yang - 0000-0003-4571-9046 - - - J, Jara-Almonte - Jara-Almonte - J - - - William, Fox - Fox - William - 0000-0001-6289-858X - - - Masaaki, Yamada - Yamada - Masaaki - 0000-0003-4996-1649 - - - Andrew, Alt - Alt - Andrew - 0000-0001-9475-8282 - - - Aaron, Goodman - Goodman - Aaron - - - - Lower Hybrid Drift Waves During Guide Field Reconnection - - Princeton University - - 2020 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DESC0016278 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-FG02-04ER54746 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-FG02-00ER54585 - - - National Aeronautics and Space Administration - https://ror.org/027ka1x80 - NNH14AX63I - - - National Aeronautics and Space Administration - https://ror.org/027ka1x80 - NNH15AB29I - - - Division of Atmospheric and Geospace Sciences - https://ror.org/037gd6g64 - AGS-1552142 - - - Division of Atmospheric and Geospace Sciences - https://ror.org/037gd6g64 - AGS-1619584 - - - National Science Foundation - https://ror.org/021nxhr62 - DE-FG02-00ER54585 - - - - ark:/88435/dsp0112579w37b - 10.1029/2020GL087192 - - 1 - - Creative Commons Attribution 4.0 International - - - - Digital data for figures used in Lower Hybrid Drift Waves During Guide - Field Reconnection, Geophysical Research Letters, 47, e2020GL087192, 2020. - - - \ No newline at end of file diff --git a/spec/system/data_migration/hybrid_drift_form_submission_spec.rb b/spec/system/data_migration/hybrid_drift_form_submission_spec.rb deleted file mode 100644 index 8a2f36b56..000000000 --- a/spec/system/data_migration/hybrid_drift_form_submission_spec.rb +++ /dev/null @@ -1,156 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating Thomson Scattering", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "Lower Hybrid Drift Waves During Guide Field Reconnection" } - let(:description) do - "Digital data for figures used in Lower Hybrid Drift Waves During Guide Field Reconnection, Geophysical Research Letters, 47, e2020GL087192, 2020." - end - let(:ark) { "ark:/88435/dsp0112579w37b" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - # DOI of this data set as found at https://www.osti.gov/pages/biblio/1814564 - let(:doi) { "10.11578/1814938" } - # This is the DOI of the paper that used this data set - let(:related_identifier) { "10.1029/2020GL087192" } - let(:related_identifier_type) { "DOI" } - let(:relation_type) { "IsCitedBy" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.11578")) - stub_request(:get, "https://handle.stage.datacite.org/10.11578/1814938") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/works/new?migrate=true" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-3881-1995" - find("tr:last-child input[name='creators[][given_name]']").set "Jongsoo" - find("tr:last-child input[name='creators[][family_name]']").set "Yoo" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Ji" - find("tr:last-child input[name='creators[][family_name]']").set "Jeong-Young" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Ambat" - find("tr:last-child input[name='creators[][family_name]']").set "M.V." - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Wang" - find("tr:last-child input[name='creators[][family_name]']").set "Shan" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-9600-9963" - find("tr:last-child input[name='creators[][given_name]']").set "Ji" - find("tr:last-child input[name='creators[][family_name]']").set "Hantao" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Lo" - find("tr:last-child input[name='creators[][family_name]']").set "Jenson" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Li" - find("tr:last-child input[name='creators[][family_name]']").set "Bowen" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-4571-9046" - find("tr:last-child input[name='creators[][given_name]']").set "Ren" - find("tr:last-child input[name='creators[][family_name]']").set "Yang" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Jara-Almonte" - find("tr:last-child input[name='creators[][family_name]']").set "J" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-6289-858X" - find("tr:last-child input[name='creators[][given_name]']").set "Fox" - find("tr:last-child input[name='creators[][family_name]']").set "William" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-4996-1649" - find("tr:last-child input[name='creators[][given_name]']").set "Yamada" - find("tr:last-child input[name='creators[][family_name]']").set "Masaaki" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-9475-8282" - find("tr:last-child input[name='creators[][given_name]']").set "Alt" - find("tr:last-child input[name='creators[][family_name]']").set "Andrew" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Goodman" - find("tr:last-child input[name='creators[][family_name]']").set "Aaron" - - # Select Additional Metadata Tab - click_on "Additional Metadata" - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][award_number]']").set "DESC0016278" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][award_number]']").set "DE-FG02-04ER54746" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][award_number]']").set "DE-FG02-00ER54585" - click_on "Add Another Funder" - # https://ror.org/027ka1x80 == ROR for National Aeronautics and Space Administration - page.find(:xpath, "//table[@id='funding']//tr[5]//input[@name='funders[][ror]']").set "https://ror.org/027ka1x80" - page.find(:xpath, "//table[@id='funding']//tr[5]//input[@name='funders[][award_number]']").set "NNH14AX63I" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[6]//input[@name='funders[][ror]']").set "https://ror.org/027ka1x80" - page.find(:xpath, "//table[@id='funding']//tr[6]//input[@name='funders[][award_number]']").set "NNH15AB29I" - click_on "Add Another Funder" - # https://ror.org/037gd6g64 == ROR for Division of Atmospheric and Geospace Sciences - page.find(:xpath, "//table[@id='funding']//tr[7]//input[@name='funders[][ror]']").set "https://ror.org/037gd6g64" - page.find(:xpath, "//table[@id='funding']//tr[7]//input[@name='funders[][award_number]']").set "AGS-1552142" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[8]//input[@name='funders[][ror]']").set "https://ror.org/037gd6g64" - page.find(:xpath, "//table[@id='funding']//tr[8]//input[@name='funders[][award_number]']").set "AGS-1619584" - click_on "Add Another Funder" - # https://ror.org/021nxhr62 == ROR for National Science Foundation - page.find(:xpath, "//table[@id='funding']//tr[9]//input[@name='funders[][ror]']").set "https://ror.org/021nxhr62" - page.find(:xpath, "//table[@id='funding']//tr[9]//input[@name='funders[][award_number]']").set "DE-FG02-00ER54585" - - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set related_identifier - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, related_identifier_type).select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - - # Select Curator Controlled Tab - click_on "Curator Controlled" - - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2020 - select group, from: "group_id" - - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - hybrid_drift_work = Work.last - expect(hybrid_drift_work.title).to eq title - expect(hybrid_drift_work.ark).to eq ark - - # Check that RORs were persisted as funder names - funders = hybrid_drift_work.resource.funders.map(&:funder_name).uniq - expect(funders).to contain_exactly("United States Department of Energy", "National Aeronautics and Space Administration", "Division of Atmospheric and Geospace Sciences", "National Science Foundation") - - # # Ensure the datacite record produced validates against our local copy of the datacite schema. - # # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(hybrid_drift_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/hybrid_drift.xml")) - export_spec_data("hybrid_drift.json", hybrid_drift_work.to_json) - end - end -end diff --git a/spec/system/data_migration/ion_orbital.xml b/spec/system/data_migration/ion_orbital.xml deleted file mode 100644 index 633052f9b..000000000 --- a/spec/system/data_migration/ion_orbital.xml +++ /dev/null @@ -1,97 +0,0 @@ - - 10.34770/tbd - - - Zhu, Hongxuan - Hongxuan - Zhu - 0000-0002-9844-6972 - - - Stoltzfus-Dueck, T - T - Stoltzfus-Dueck - 0000-0003-2587-6298 - - - Hager, R - R - Hager - 0000-0002-4624-3150 - - - Ku, S - S - Ku - 0000-0002-9964-1208 - - - Chang, C.S. - C.S. - Chang - 0000-0002-3346-5731 - - - - - Effects of collisional ion orbit loss on tokamak radial electric field and - toroidal rotation in an L-mode plasma - - - Princeton University - - 2023 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02- 05CH11231 - - - United States Department of Energy - https://ror.org/01bj3aw27 - SciDAC-4 - - - Princeton University - https://ror.org/00hx57361 - n/a - - - - ark:/88435/dsp01r494vp42z - 10.1088/1741-4326/acc815 - - 1 - - Creative Commons Attribution 4.0 International - - - - Ion orbit loss has been used to model the formation of a strong negative - radial electric field Er in the tokamak edge, as well as edge momentum - transport and toroidal rotation. To quantitatively measure ion orbit loss, - an orbit-flux formulation has been developed and numerically applied to - the gyrokinetic particle-in-cell code XGC. We study collisional ion orbit - loss in an axisymmetric DIII-D L-mode plasma using gyrokinetic ions and - drift-kinetic electrons. Numerical simulations, where the plasma density - and temperature profiles are maintained through neutral ionization and - heating, show the formation of a quasisteady negative Er in the edge. We - have measured a radially outgoing ion gyrocenter flux due to collisional - scattering of ions into the loss orbits, which is balanced by the radially - incoming ion gyrocenter flux from confined orbits on the collisional time - scale. This suggests that collisional ion orbit loss can shift Er in the - negative direction compared to that in plasmas without orbit loss. It is - also found that collisional ion orbit loss can contribute to a radially - outgoing (counter-current) toroidal-angular-momentum flux, which is not - balanced by the toroidal-angular-momentum flux carried by ions on the - confined orbits. Therefore, the edge toroidal rotation shifts in the - co-current direction on the collisional time scale. - - - \ No newline at end of file diff --git a/spec/system/data_migration/ion_orbital_form_submission_spec.rb b/spec/system/data_migration/ion_orbital_form_submission_spec.rb deleted file mode 100644 index c4e360390..000000000 --- a/spec/system/data_migration/ion_orbital_form_submission_spec.rb +++ /dev/null @@ -1,99 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for ion orbital", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "Effects of collisional ion orbit loss on tokamak radial electric field and toroidal rotation in an L-mode plasma" } - let(:description) do - "Ion orbit loss has been used to model the formation of a strong negative radial electric field Er in the tokamak edge, as well as edge momentum transport and toroidal rotation. To quantitatively measure ion orbit loss, an orbit-flux formulation has been developed and numerically applied to the gyrokinetic particle-in-cell code XGC. We study collisional ion orbit loss in an axisymmetric DIII-D L-mode plasma using gyrokinetic ions and drift-kinetic electrons. Numerical simulations, where the plasma density and temperature profiles are maintained through neutral ionization and heating, show the formation of a quasisteady negative Er in the edge. We have measured a radially outgoing ion gyrocenter flux due to collisional scattering of ions into the loss orbits, which is balanced by the radially incoming ion gyrocenter flux from confined orbits on the collisional time scale. This suggests that collisional ion orbit loss can shift Er in the negative direction compared to that in plasmas without orbit loss. It is also found that collisional ion orbit loss can contribute to a radially outgoing (counter-current) toroidal-angular-momentum flux, which is not balanced by the toroidal-angular-momentum flux carried by ions on the confined orbits. Therefore, the edge toroidal rotation shifts in the co-current direction on the collisional time scale." - end - let(:ark) { "ark:/88435/dsp01r494vp42z" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/tbd" } - let(:related_identifier) { "10.1088/1741-4326/acc815" } - let(:related_identifier_type) { "DOI" } - let(:relation_type) { "IsCitedBy" } - let(:keywords) { "ion orbit loss, radial electric field, tokamak edge plasmas, gyrokinetic simulations" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.11578")) - stub_request(:get, "https://handle.stage.datacite.org/#{doi}") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/works/new?migrate=true" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-9844-6972" - find("tr:last-child input[name='creators[][given_name]']").set "Hongxuan" - find("tr:last-child input[name='creators[][family_name]']").set "Zhu" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-2587-6298" - find("tr:last-child input[name='creators[][given_name]']").set "T" - find("tr:last-child input[name='creators[][family_name]']").set "Stoltzfus-Dueck" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-4624-3150" - find("tr:last-child input[name='creators[][given_name]']").set "R" - find("tr:last-child input[name='creators[][family_name]']").set "Hager" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-9964-1208" - find("tr:last-child input[name='creators[][given_name]']").set "S" - find("tr:last-child input[name='creators[][family_name]']").set "Ku" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-3346-5731" - find("tr:last-child input[name='creators[][given_name]']").set "C.S." - find("tr:last-child input[name='creators[][family_name]']").set "Chang" - - click_on "Additional Metadata" - - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set related_identifier - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, related_identifier_type).select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][award_number]']").set "DE-AC02- 05CH11231" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][award_number]']").set "SciDAC-4" - click_on "Add Another Funder" - # https://ror.org/00hx57361 == ROR for Princeton University - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][ror]']").set "https://ror.org/00hx57361" - page.find(:xpath, "//table[@id='funding']//tr[4]//input[@name='funders[][award_number]']").set "n/a" - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2023 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - ion_orbital_work = Work.last - expect(ion_orbital_work.title).to eq title - expect(ion_orbital_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(ion_orbital_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/ion_orbital.xml")) - export_spec_data("ion_orbital.json", ion_orbital_work.to_json) - end - end -end diff --git a/spec/system/data_migration/non_axisymmetric.xml b/spec/system/data_migration/non_axisymmetric.xml deleted file mode 100644 index bee524cce..000000000 --- a/spec/system/data_migration/non_axisymmetric.xml +++ /dev/null @@ -1,92 +0,0 @@ - - 10.11578/1888269 - - - Wang, Yin - Yin - Wang - 0000-0002-6572-4902 - - - Gilson, Erik P. - Erik P. - Gilson - 0000-0001-6820-9132 - - - Ebrahimi, Fatima - Fatima - Ebrahimi - 0000-0003-3109-5367 - - - Goodman, Jeremy - Jeremy - Goodman - 0000-0002-6710-7748 - - - Caspary, Kyle J. - Kyle J. - Caspary - 0000-0002-5441-7309 - - - Winarto, Himawan W. - Himawan W. - Winarto - 0000-0002-0697-7985 - - - Ji, Hantao - Hantao - Ji - 0000-0001-9600-9963 - - - - - Identification of a non-axisymmetric mode in laboratory experiments - searching for standard magnetorotational instability - - - Princeton University - - 2022 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - National Science Foundation - https://ror.org/021nxhr62 - AST-2108871 - - - National Aeronautics and Space Administration - https://ror.org/027ka1x80 - NNH15AB25I - - - - ark:/88435/dsp01sx61dq46q - 10.1038/s41467-022-32278-0 - - 1 - - Creative Commons Attribution 4.0 International - - - - This dataset provides the source data of figures in the main text of the - paper Identification of a non-axisymmetric mode in laboratory experiments - searching for standard magnetorotational instability accepted by Nature - Communications. File name: SourceData.xlsx Description: source data for - the 8 figures in the main text of the paper Identification of a - non-axisymmetric mode in laboratory experiments searching for standard - magnetorotational instability accepted by Nature Communications. - - - \ No newline at end of file diff --git a/spec/system/data_migration/non_axisymmetric_form_submission_spec.rb b/spec/system/data_migration/non_axisymmetric_form_submission_spec.rb deleted file mode 100644 index befadfc10..000000000 --- a/spec/system/data_migration/non_axisymmetric_form_submission_spec.rb +++ /dev/null @@ -1,108 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for non_axisymmetric", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "Identification of a non-axisymmetric mode in laboratory experiments searching for standard magnetorotational instability" } - let(:description) do - "This dataset provides the source data of figures in the main text of the paper Identification of a non-axisymmetric mode in laboratory experiments searching for standard magnetorotational instability accepted by Nature Communications. - -File name: SourceData.xlsx Description: source data for the 8 figures in the main text of the paper Identification of a non-axisymmetric mode in laboratory experiments searching for standard magnetorotational instability accepted by Nature Communications." - end - let(:ark) { "ark:/88435/dsp01sx61dq46q" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.11578/1888269" } - let(:related_identifier) { "10.1038/s41467-022-32278-0" } - let(:related_identifier_type) { "DOI" } - let(:relation_type) { "IsCitedBy" } - let(:keywords) { "magnetorotational instability, MRI, liquid metal, taylor-couette flow," } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.11578")) - stub_request(:get, "https://handle.stage.datacite.org/#{doi}") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/works/new?migrate=true" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-6572-4902" - find("tr:last-child input[name='creators[][given_name]']").set "Yin" - find("tr:last-child input[name='creators[][family_name]']").set "Wang" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-6820-9132" - find("tr:last-child input[name='creators[][given_name]']").set "Erik P." - find("tr:last-child input[name='creators[][family_name]']").set "Gilson" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-3109-5367" - find("tr:last-child input[name='creators[][given_name]']").set "Fatima" - find("tr:last-child input[name='creators[][family_name]']").set "Ebrahimi" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-6710-7748" - find("tr:last-child input[name='creators[][given_name]']").set "Jeremy" - find("tr:last-child input[name='creators[][family_name]']").set "Goodman" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-5441-7309" - find("tr:last-child input[name='creators[][given_name]']").set "Kyle J." - find("tr:last-child input[name='creators[][family_name]']").set "Caspary" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-0697-7985" - find("tr:last-child input[name='creators[][given_name]']").set "Himawan W." - find("tr:last-child input[name='creators[][family_name]']").set "Winarto" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-9600-9963" - find("tr:last-child input[name='creators[][given_name]']").set "Hantao" - find("tr:last-child input[name='creators[][family_name]']").set "Ji" - - click_on "Additional Metadata" - - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set related_identifier - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, related_identifier_type).select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - click_on "Add Another Funder" - # https://ror.org/021nxhr62 == ROR for National Science Foundation - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][ror]']").set "https://ror.org/021nxhr62" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][award_number]']").set "AST-2108871" - click_on "Add Another Funder" - # https://ror.org/027ka1x80 == ROR for National Aeronautics and Space Administration - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][ror]']").set "https://ror.org/027ka1x80" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][award_number]']").set "NNH15AB25I" - - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2022 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - non_axisymmetric_work = Work.last - expect(non_axisymmetric_work.title).to eq title - expect(non_axisymmetric_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(non_axisymmetric_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/non_axisymmetric.xml")) - export_spec_data("non_axisymmetric.json", non_axisymmetric_work.to_json) - end - end -end diff --git a/spec/system/data_migration/observation_axisymmetric.xml b/spec/system/data_migration/observation_axisymmetric.xml deleted file mode 100644 index 5cec2b8dd..000000000 --- a/spec/system/data_migration/observation_axisymmetric.xml +++ /dev/null @@ -1,78 +0,0 @@ - - 10.11578/1888278 - - - Wang, Yin - Yin - Wang - 0000-0002-6572-4902 - - - Gilson, Erik - Erik - Gilson - 0000-0001-6820-9132 - - - Ebrahimi, Fatima - Fatima - Ebrahimi - 0000-0003-3109-5367 - - - Goodman, Jeremy - Jeremy - Goodman - 0000-0002-6710-7748 - - - Ji, Hantao - Hantao - Ji - 0000-0001-9600-9963 - - - - - Source data for Observation of Axisymmetric Standard Magnetorotational - Instability in the Laboratory - - - Princeton University - - 2022 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - National Science Foundation - https://ror.org/021nxhr62 - AST-2108871 - - - National Aeronautics and Space Administration - https://ror.org/027ka1x80 - NNH15AB25I - - - - ark:/88435/dsp018623j1954 - 10.1103/PhysRevLett.129.115001 - - 1 - - Creative Commons Attribution 4.0 International - - - - Source data for the article Observation of Axisymmetric Standard - Magnetorotational Instability in the Laboratory published in Physical - Review Letters. Source data for Figure 2, Figure 4, Figure 5 and Figure 7 - of the article Observation of Axisymmetric Standard Magnetorotational - Instability in the Laboratory published in Physical Review Letters. - - - \ No newline at end of file diff --git a/spec/system/data_migration/observation_axisymmetric_form_submission_spec.rb b/spec/system/data_migration/observation_axisymmetric_form_submission_spec.rb deleted file mode 100644 index d49dcae16..000000000 --- a/spec/system/data_migration/observation_axisymmetric_form_submission_spec.rb +++ /dev/null @@ -1,100 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for observation-axisymmetric", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "Source data for Observation of Axisymmetric Standard Magnetorotational Instability in the Laboratory" } - let(:description) do - "Source data for the article Observation of Axisymmetric Standard Magnetorotational Instability in the Laboratory published in Physical Review Letters. - -Source data for Figure 2, Figure 4, Figure 5 and Figure 7 of the article Observation of Axisymmetric Standard Magnetorotational Instability in the Laboratory published in Physical Review Letters." - end - let(:ark) { "ark:/88435/dsp018623j1954" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.11578/1888278" } - let(:related_identifier) { "10.1103/PhysRevLett.129.115001" } - let(:related_identifier_type) { "DOI" } - let(:relation_type) { "IsCitedBy" } - let(:keywords) { "magnetorotational instability, taylor-couette flow, liquid metal, mhd instability, accretion disk" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.11578")) - stub_request(:get, "https://handle.stage.datacite.org/10.11578/1888278") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/works/new?migrate=true" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-6572-4902" - find("tr:last-child input[name='creators[][given_name]']").set "Yin" - find("tr:last-child input[name='creators[][family_name]']").set "Wang" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-6820-9132" - find("tr:last-child input[name='creators[][given_name]']").set "Erik" - find("tr:last-child input[name='creators[][family_name]']").set "Gilson" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-3109-5367" - find("tr:last-child input[name='creators[][given_name]']").set "Fatima" - find("tr:last-child input[name='creators[][family_name]']").set "Ebrahimi" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-6710-7748" - find("tr:last-child input[name='creators[][given_name]']").set "Jeremy" - find("tr:last-child input[name='creators[][family_name]']").set "Goodman" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-9600-9963" - find("tr:last-child input[name='creators[][given_name]']").set "Hantao" - find("tr:last-child input[name='creators[][family_name]']").set "Ji" - - click_on "Additional Metadata" - - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set related_identifier - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, related_identifier_type).select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - click_on "Add Another Funder" - # https://ror.org/021nxhr62 == ROR for National Science Foundation - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][ror]']").set "https://ror.org/021nxhr62" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][award_number]']").set "AST-2108871" - click_on "Add Another Funder" - # https://ror.org/027ka1x80 == ROR for National Aeronautics and Space Administration - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][ror]']").set "https://ror.org/027ka1x80" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][award_number]']").set "NNH15AB25I" - - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2022 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - observation_axisymmetric_work = Work.last - expect(observation_axisymmetric_work.title).to eq title - expect(observation_axisymmetric_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(observation_axisymmetric_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/observation_axisymmetric.xml")) - export_spec_data("observation_axisymmetric.json", observation_axisymmetric_work.to_json) - end - end -end diff --git a/spec/system/data_migration/sowingseeds.xml b/spec/system/data_migration/sowingseeds.xml deleted file mode 100644 index 0c11a63dd..000000000 --- a/spec/system/data_migration/sowingseeds.xml +++ /dev/null @@ -1,76 +0,0 @@ - - 10.34770/doc-1 - - - Abrams, Samantha - Samantha - Abrams - - - Antracoli, Alexis - Alexis - Antracoli - - - Appel, Rachel - Rachel - Appel - - - Caust-Ellenbogen, Celia - Celia - Caust-Ellenbogen - - - Dennison, Sarah - Sarah - Dennison - - - Duncan, Sumitra - Sumitra - Duncan - - - Ramsay, Stefanie - Stefanie - Ramsay - - - - Sowing the Seeds for More Usable Web Archives: A Usability Study of Archive-It - - Princeton University - - 2023 - - ark:/88435/dsp01d791sj97j - - 1 - - Creative Commons Attribution 4.0 International - - - - In 2017, seven members of the Archive-It Mid-Atlantic Users Group (AITMA) - conducted a study of 14 subjects representative of their stakeholder - populations to assess the usability of Archive-It, a web archiving - subscription service of the Internet Archive. While Archive-It is the most - widely-used tool for web archiving, little is known about how users - interact with the service. This study intended to teach us what users - expect from web archives, which exist as another form of archival - material. End-user subjects executed four search tasks using the public - Archive-It interface and the Wayback Machine to access archived - information on websites from the facilitators' own harvested - collections and provide feedback about their experiences. The tasks were - designed to have straightforward pass or fail outcomes, and the - facilitators took notes on the subjects' behavior and commentary - during the sessions. Overall, participants reported mildly positive - impressions of Archive-It public user interface based on their session. - The study identified several key areas of improvement for the Archive-It - service pertaining to metadata options, terminology display, indexing of - dates, and the site's search box. Download the README.txt for a - detailed description of this dataset's content. - - - \ No newline at end of file diff --git a/spec/system/data_migration/sowingseeds_form_submission_spec.rb b/spec/system/data_migration/sowingseeds_form_submission_spec.rb deleted file mode 100644 index 5da5e0e0e..000000000 --- a/spec/system/data_migration/sowingseeds_form_submission_spec.rb +++ /dev/null @@ -1,93 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating bitklavier", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "Sowing the Seeds for More Usable Web Archives: A Usability Study of Archive-It" } - let(:description) do - "In 2017, seven members of the Archive-It Mid-Atlantic Users Group (AITMA) conducted a study of 14 subjects representative of their stakeholder populations to assess the usability of Archive-It, a web archiving subscription service of the Internet Archive. While Archive-It is the most widely-used tool for web archiving, little is known about how users interact with the service. This study intended to teach us what users expect from web archives, which exist as another form of archival material. End-user subjects executed four search tasks using the public Archive-It interface and the Wayback Machine to access archived information on websites from the facilitators' own harvested collections and provide feedback about their experiences. The tasks were designed to have straightforward pass or fail outcomes, -and the facilitators took notes on the subjects' behavior and commentary during the sessions. Overall, participants reported mildly positive impressions of Archive-It public user interface based on their session. The study identified several key areas of improvement for the Archive-It service pertaining to metadata options, terminology display, indexing of dates, and the site's search box. - -Download the README.txt for a detailed description of this dataset's content." - end - let(:ark) { "ark:/88435/dsp01d791sj97j" } - let(:publisher) { "Princeton University" } - let(:doi) {} - let(:file1) { Pathname.new(fixture_path).join("dataspace_migration", "sowingseeds", "readmearchiveitusability.rtf").to_s } - let(:file2) { Pathname.new(fixture_path).join("dataspace_migration", "sowingseeds", "Archive-It-UsabilityTestDataAnalysis-2017.xlsx").to_s } - let(:bucket_url) do - "https://example-bucket.s3.amazonaws.com/" - end - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/r75s-9j74") - .to_return(status: 200, body: "", headers: {}) - stub_request(:put, /#{bucket_url}/).to_return(status: 200) - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - stub_s3 - sign_in user - # we need to use the wizard because this work does not have a doi and it needs one to be registered - visit "/works/new?migrate=true" - fill_in "title_main", with: title - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Samantha" - find("tr:last-child input[name='creators[][family_name]']").set "Abrams" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Alexis" - find("tr:last-child input[name='creators[][family_name]']").set "Antracoli" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Rachel" - find("tr:last-child input[name='creators[][family_name]']").set "Appel" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Celia" - find("tr:last-child input[name='creators[][family_name]']").set "Caust-Ellenbogen" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Sarah" - find("tr:last-child input[name='creators[][family_name]']").set "Dennison" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Sumitra" - find("tr:last-child input[name='creators[][family_name]']").set "Duncan" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Stefanie" - find("tr:last-child input[name='creators[][family_name]']").set "Ramsay" - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - # TODO: We should also test that the files are saved - # See https://github.com/pulibrary/pdc_describe/issues/1041 - attach_file_via_uppy(file1) - attach_file_via_uppy(file2) - - click_on "Additional Metadata" - click_on "Curator Controlled" - fill_in "ark", with: ark - fill_in "publication_year", with: "2023" - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - click_on "Complete" - click_on "Sowing the Seeds for More Usable Web Archives: A Usability Study of Archive-It" - - # the work has been submitted and is awaiting_approval - expect(page).to have_content "Awaiting Approval" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - sowingseeds_work = Work.last - expect(sowingseeds_work.title).to eq title - expect(sowingseeds_work.ark).to eq ark - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(sowingseeds_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/sowingseeds.xml")) - export_spec_data("sowingseeds.json", sowingseeds_work.to_json) - end - end -end diff --git a/spec/system/data_migration/spindle.xml b/spec/system/data_migration/spindle.xml deleted file mode 100644 index 4f69ee8fa..000000000 --- a/spec/system/data_migration/spindle.xml +++ /dev/null @@ -1,66 +0,0 @@ - - 10.34770/qyrs-vg25 - - - Antony, James W. - James W. - Antony - - - Piloto, Luis - Luis - Piloto - - - Wang, Margaret - Margaret - Wang - - - Brooks, Paula P. - Paula P. - Brooks - - - Norman, Kenneth A - Kenneth A - Norman - - - Paller, Ken A - Ken A - Paller - - - - Sleep spindle refractoriness segregates periods of memory reactivation - - Princeton University - - 2018 - - ark:/88435/dsp011z40kw63j - - 1 - - Creative Commons Attribution 4.0 International - - - - The stability of long-term memories is enhanced by reactivation during - sleep. Correlative evidence has linked memory reactivation with - thalamocortical sleep spindles, although their functional role is not - fully understood. Our initial study replicated this correlation and also - demonstrated a novel rhythmicity to spindles, such that a spindle is more - likely to occur approximately 3–6 s following a prior spindle. We - leveraged this rhythmicity to test the role of spindles in memory by using - real-time spindle tracking to present cues within versus just after the - presumptive refractory period; as predicted, cues presented just after the - refractory period led to better memory. Our findings demonstrate a precise - temporal link between sleep spindles and memory reactivation. Moreover, - they reveal a previously undescribed neural mechanism whereby spindles may - segment sleep into two distinct substates: prime opportunities for - reactivation and gaps that segregate reactivation events. - - - \ No newline at end of file diff --git a/spec/system/data_migration/spindle_form_submission_spec.rb b/spec/system/data_migration/spindle_form_submission_spec.rb deleted file mode 100644 index 71427729d..000000000 --- a/spec/system/data_migration/spindle_form_submission_spec.rb +++ /dev/null @@ -1,79 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating Sleeo spindle", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:research_data_moderator) } - let(:title) { "Sleep spindle refractoriness segregates periods of memory reactivation" } - let(:description) do - "The stability of long-term memories is enhanced by reactivation during sleep. Correlative evidence has linked memory reactivation with thalamocortical sleep spindles, although their functional role is not fully understood. Our initial study replicated this correlation and also demonstrated a novel rhythmicity to spindles, such that a spindle is more likely to occur approximately 3–6 s following a prior spindle. We leveraged this rhythmicity to test the role of spindles in memory by using real-time spindle tracking to present cues within versus just after the presumptive refractory period; as predicted, cues presented just after the refractory period led to better memory. Our findings demonstrate a precise temporal link between sleep spindles and memory reactivation. Moreover, they reveal a previously undescribed neural mechanism whereby spindles may segment sleep into two distinct substates: prime opportunities for reactivation and gaps that segregate reactivation events." - end - let(:ark) { "ark:/88435/dsp011z40kw63j" } - let(:group) { "Research Data" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.34770/qyrs-vg25" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.34770")) - stub_request(:get, "https://handle.stage.datacite.org/10.34770/qyrs-vg25") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/works/new?migrate=true" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "James W." - find("tr:last-child input[name='creators[][family_name]']").set "Antony" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Luis" - find("tr:last-child input[name='creators[][family_name]']").set "Piloto" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Margaret" - find("tr:last-child input[name='creators[][family_name]']").set "Wang" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Paula P." - find("tr:last-child input[name='creators[][family_name]']").set "Brooks" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Kenneth A" - find("tr:last-child input[name='creators[][family_name]']").set "Norman" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Ken A" - find("tr:last-child input[name='creators[][family_name]']").set "Paller" - click_on "Additional Metadata" - # Select Additional Metadata Tab - click_on "Additional Metadata" - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2018 - fill_in "doi", with: doi - fill_in "ark", with: ark - select group, from: "group_id" - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - spindle_work = Work.last - expect(spindle_work.title).to eq title - expect(spindle_work.group).to eq Group.research_data - expect(spindle_work.ark).to eq ark - export_spec_data("spindle.json", spindle_work.to_json) - - # Ensure the datacite record produced validates against our local copy of the datacite schema. - # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(spindle_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/spindle.xml")) - end - end -end diff --git a/spec/system/data_migration/thomson_scattering.xml b/spec/system/data_migration/thomson_scattering.xml deleted file mode 100644 index 54477ab8c..000000000 --- a/spec/system/data_migration/thomson_scattering.xml +++ /dev/null @@ -1,131 +0,0 @@ - - 10.11578/1814942 - - - Hammond, K.C. - K.C. - Hammond - 0000-0002-1104-4434 - - - Laggner, F.M. - F.M. - Laggner - 0000-0003-1601-2973 - - - Diallo, A. - A. - Diallo - 0000-0002-0706-060X - - - Doskoczynski, S. - S. - Doskoczynski - - - Freeman, C. - C. - Freeman - - - Funaba, H. - H. - Funaba - - - Gates, D.A. - D.A. - Gates - 0000-0001-5679-3124 - - - Rozenblat, R. - R. - Rozenblat - - - Tchilinguirian, G. - G. - Tchilinguirian - 0000-0002-8014-5212 - - - Xing, Z. - Z. - Xing - - - Yamada, I. - I. - Yamada - - - Yasuhara, R. - R. - Yasuhara - - - Zimmer, G - G - Zimmer - 0000-0002-1992-5121 - - - Kolemen, E. - E. - Kolemen - 0000-0003-4212-3247 - - - - - Initial operation and data processing on a system for real-time evaluation - of Thomson scattering signals on the Large Helical Device - - - Princeton University - - 2021 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-AC02-09CH11466 - - - United States Department of Energy - https://ror.org/01bj3aw27 - DE-SC0015480 - - - National Institute for Fusion Science - https://ror.org/01t3wyv61 - ULHH040 - - - - ark:/88435/dsp014t64gr25v - 10.1063/5.0041507 - - 1 - - Creative Commons Attribution 4.0 International - - - - A scalable system for real-time analysis of electron temperature and - density based on signals from the Thomson scattering diagnostic, initially - developed for and installed on the NSTX-U experiment, was recently adapted - for the Large Helical Device (LHD) and operated for the first time during - plasma discharges. During its initial operation run, it routinely recorded - and processed signals for four spatial points at the laser repetition rate - of 30 Hz, well within the system's rated capability for 60 Hz. We - present examples of data collected from this initial run and describe - subsequent adaptations to the analysis code to improve the fidelity of the - temperature calculations. Please consult the file README.txt for a - description of the archive contents. - - - \ No newline at end of file diff --git a/spec/system/data_migration/thomson_scattering_form_submission_spec.rb b/spec/system/data_migration/thomson_scattering_form_submission_spec.rb deleted file mode 100644 index 2d11e461d..000000000 --- a/spec/system/data_migration/thomson_scattering_form_submission_spec.rb +++ /dev/null @@ -1,139 +0,0 @@ -# frozen_string_literal: true -require "rails_helper" - -RSpec.describe "Form submission for migrating Thomson Scattering", type: :system, mock_ezid_api: true, js: true do - let(:user) { FactoryBot.create(:pppl_moderator) } - let(:title) { "Initial operation and data processing on a system for real-time evaluation of Thomson scattering signals on the Large Helical Device" } - let(:description) do - "A scalable system for real-time analysis of electron temperature and density based on signals from the Thomson scattering diagnostic, initially developed for and installed on the NSTX-U experiment, was recently adapted for the Large Helical Device (LHD) and operated for the first time during plasma discharges. During its initial operation run, it routinely recorded and processed signals for four spatial points at the laser repetition rate of 30 Hz, well within the system's rated capability for 60 Hz. We present examples of data collected from this initial run and describe subsequent adaptations to the analysis code to improve the fidelity of the temperature calculations. - -Please consult the file README.txt for a description of the archive contents." - end - let(:ark) { "ark:/88435/dsp014t64gr25v" } - let(:group) { "Princeton Plasma Physics Lab (PPPL)" } - let(:publisher) { "Princeton University" } - let(:doi) { "10.11578/1814942" } - let(:related_identifier) { "10.1063/5.0041507" } - let(:related_identifier_type) { "DOI" } - let(:relation_type) { "IsCitedBy" } - - let(:keywords) { "Thomson scattering, real-time, LHD, plasma diagnostic" } - - before do - stub_datacite(host: "api.datacite.org", body: datacite_register_body(prefix: "10.11578")) - stub_request(:get, "https://handle.stage.datacite.org/#{doi}") - .to_return(status: 200, body: "", headers: {}) - stub_s3 - end - context "migrate record from dataspace" do - it "produces and saves a valid datacite record" do - sign_in user - visit "/works/new?migrate=true" - fill_in "title_main", with: title - fill_in "description", with: description - select "Creative Commons Attribution 4.0 International", from: "rights_identifiers" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-1104-4434" - find("tr:last-child input[name='creators[][given_name]']").set "K.C." - find("tr:last-child input[name='creators[][family_name]']").set "Hammond" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-1601-2973" - find("tr:last-child input[name='creators[][given_name]']").set "F.M." - find("tr:last-child input[name='creators[][family_name]']").set "Laggner" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-0706-060X" - find("tr:last-child input[name='creators[][given_name]']").set "A." - find("tr:last-child input[name='creators[][family_name]']").set "Diallo" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "S." - find("tr:last-child input[name='creators[][family_name]']").set "Doskoczynski" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "C." - find("tr:last-child input[name='creators[][family_name]']").set "Freeman" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "H." - find("tr:last-child input[name='creators[][family_name]']").set "Funaba" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0001-5679-3124" - find("tr:last-child input[name='creators[][given_name]']").set "D.A." - find("tr:last-child input[name='creators[][family_name]']").set "Gates" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "R." - find("tr:last-child input[name='creators[][family_name]']").set "Rozenblat" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-8014-5212" - find("tr:last-child input[name='creators[][given_name]']").set "G." - find("tr:last-child input[name='creators[][family_name]']").set "Tchilinguirian" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "Z." - find("tr:last-child input[name='creators[][family_name]']").set "Xing" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "I." - find("tr:last-child input[name='creators[][family_name]']").set "Yamada" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "" - find("tr:last-child input[name='creators[][given_name]']").set "R." - find("tr:last-child input[name='creators[][family_name]']").set "Yasuhara" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0002-1992-5121" - find("tr:last-child input[name='creators[][given_name]']").set "G" - find("tr:last-child input[name='creators[][family_name]']").set "Zimmer" - click_on "Add Another Creator" - find("tr:last-child input[name='creators[][orcid]']").set "0000-0003-4212-3247" - find("tr:last-child input[name='creators[][given_name]']").set "E." - find("tr:last-child input[name='creators[][family_name]']").set "Kolemen" - - click_on "Additional Metadata" - - # Related Objects - find("tr:last-child input[name='related_objects[][related_identifier]']").set related_identifier - find("tr:last-child select[name='related_objects[][related_identifier_type]']").find(:option, related_identifier_type).select_option - find("tr:last-child select[name='related_objects[][relation_type]']").find(:option, relation_type).select_option - - fill_in "keywords", with: keywords - - ## Funder Information - # https://ror.org/01bj3aw27 == ROR for United States Department of Energy - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[1]//input[@name='funders[][award_number]']").set "DE-AC02-09CH11466" - click_on "Add Another Funder" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][ror]']").set "https://ror.org/01bj3aw27" - page.find(:xpath, "//table[@id='funding']//tr[2]//input[@name='funders[][award_number]']").set "DE-SC0015480" - click_on "Add Another Funder" - # https://ror.org/01t3wyv61 == ROR for National Institute for Fusion Science - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][ror]']").set "https://ror.org/01t3wyv61" - page.find(:xpath, "//table[@id='funding']//tr[3]//input[@name='funders[][award_number]']").set "ULHH040" - click_on "Curator Controlled" - fill_in "publisher", with: publisher - fill_in "publication_year", with: 2021 - select group, from: "group_id" - fill_in "doi", with: doi - fill_in "ark", with: ark - click_on "Migrate" - expect(page).to have_button("Migrate Dataspace Files") - expect(page).to have_content "marked as Draft" - expect(page).to have_content "Creative Commons Attribution 4.0 International" - click_on "Complete" - expect(page).to have_content "awaiting_approval" - thomson_scattering_work = Work.last - expect(thomson_scattering_work.title).to eq title - expect(thomson_scattering_work.ark).to eq ark - - # Check that RORs were persisted as funder names - funders = thomson_scattering_work.resource.funders.map(&:funder_name).uniq - expect(funders).to contain_exactly("United States Department of Energy", "National Institute for Fusion Science") - - # # Ensure the datacite record produced validates against our local copy of the datacite schema. - # # This will allow us to evolve our local datacite standards and test our records against them. - datacite = PDCSerialization::Datacite.new_from_work(thomson_scattering_work) - expect(datacite.valid?).to eq true - expect(datacite.to_xml).to be_equivalent_to(File.read("spec/system/data_migration/thomson_scattering.xml")) - export_spec_data("thomson_scattering.json", thomson_scattering_work.to_json) - end - end -end