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Polyphemus mvir1 waiver update json #1016

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merged 3 commits into from
Sep 8, 2022
Merged

Polyphemus mvir1 waiver update json #1016

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1963260
use update_json instead of update for cascade waiver etl
coleshaw Sep 8, 2022
6d8be83
update specs
coleshaw Sep 8, 2022
713dc33
update poetry version
coleshaw Sep 8, 2022
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2 changes: 1 addition & 1 deletion docker/archimedes-base/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ WORKDIR /app
ENV DOCKER_VERSION 19.03.12
ENV PYTHON_VERSION 3.8
ENV DOCKERIZE_VERSION 0.5.0
ENV POETRY_VERSION 1.1.4
ENV POETRY_VERSION 1.1.15
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Looks like we hit this problem: python-poetry/poetry#6300

So bumping the poetry version.

ENV DOCKERIZE_URL https://github.com/jwilder/dockerize/releases/download/v${DOCKERIZE_VERSION}/dockerize-linux-amd64-v${DOCKERIZE_VERSION}.tar.gz
ENV PATH "/app/bin:/opt/poetry/bin:$PATH"
ENV POETRY_HOME "/opt/poetry"
Expand Down
8 changes: 4 additions & 4 deletions polyphemus/lib/commands.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -310,7 +310,7 @@ def cascade_to_pool(base_model)

update_request = Etna::Clients::Magma::UpdateRequest.new(project_name: project)
update_request.update_revision("#{base_model}_pool", pool, restricted: true)
magma_client.update(update_request)
magma_client.update_json(update_request)
else
logger.info "#{base_model}_pool #{pool} does not include a restricted patient, relaxing."

Expand All @@ -322,7 +322,7 @@ def cascade_to_pool(base_model)

update_request = Etna::Clients::Magma::UpdateRequest.new(project_name: project)
update_request.update_revision("#{base_model}_pool", pool, restricted: false)
magma_client.update(update_request)
magma_client.update_json(update_request)
end
end
end
Expand All @@ -341,7 +341,7 @@ def restrict!(patient, delete_metis_files: false)
Rollbar.info("Attempting to restrict access to #{name}")
update_request = Etna::Clients::Magma::UpdateRequest.new(project_name: project)
update_request.update_revision('patient', name, restricted: true)
magma_client.update(update_request)
magma_client.update_json(update_request)
end
end

Expand All @@ -362,7 +362,7 @@ def unrestrict!(patient)
Rollbar.info("Attempting to unrestrict access to #{name}")
update_request = Etna::Clients::Magma::UpdateRequest.new(project_name: project)
update_request.update_revision('patient', name, restricted: false)
magma_client.update(update_request)
magma_client.update_json(update_request)
end
end

Expand Down
30 changes: 15 additions & 15 deletions polyphemus/spec/cascade_mvir_restricted_spec.rb
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Expand Up @@ -14,7 +14,7 @@
@all_updates = []

WebMock.disable_net_connect!
stub_magma_setup(patients_to_restrict)
stub_magma_setup(patients_to_restrict, use_json: true)
stub_magma_restricted_pools('cytof', ['pool-a', 'pool-c'])
stub_magma_all_pools('cytof', ['pool-a', 'pool-c'])
stub_magma_restricted_pools('sc_rna_seq', ['pool-e', 'pool-f'])
Expand Down Expand Up @@ -53,23 +53,23 @@
acc
end).to eq({
"cytof_pool" => {
"pool-a" => {"restricted" => "true"},
"pool-c" => {"restricted" => "true"}
"pool-a" => {"restricted" => true},
"pool-c" => {"restricted" => true}
},
"sc_rna_seq_pool" => {
"pool-e" => {"restricted" => "true"},
"pool-f" => {"restricted" => "true"},
"pool-e" => {"restricted" => true},
"pool-f" => {"restricted" => true},
},
"patient" => {
"Mike" => {"restricted" => "true"},
"Dan" => {"restricted" => "true"},
"Mike" => {"restricted" => true},
"Dan" => {"restricted" => true},
}
})
end

it 'correctly makes Metis calls to restrict patient and pool folders' do
patients_to_restrict[:Dan][:consent] = 'No Samples/Data'
stub_magma_setup(patients_to_restrict)
stub_magma_setup(patients_to_restrict, use_json: true)

stub_parent_exists({status: 422, bucket: RESTRICT_BUCKET})
stub_create_folder({bucket: RESTRICT_BUCKET})
Expand Down Expand Up @@ -119,7 +119,7 @@

it 'continues working if a single patient throws an error' do
patients_to_restrict[:Dan][:consent] = 'No Samples/Data'
stub_magma_setup(patients_to_restrict)
stub_magma_setup(patients_to_restrict, use_json: true)
stub_parent_exists({status: 422, bucket: RESTRICT_BUCKET})
stub_create_folder({bucket: RESTRICT_BUCKET})
stub_rename_folder_with_error({bucket: RELEASE_BUCKET})
Expand Down Expand Up @@ -176,7 +176,7 @@

WebMock.disable_net_connect!

stub_magma_setup(patients_to_release)
stub_magma_setup(patients_to_release, use_json: true)
stub_magma_restricted_pools('cytof', [])
stub_magma_restricted_pools('sc_rna_seq', [])
stub_magma_all_pools('cytof', ['pool-b', 'pool-d'])
Expand Down Expand Up @@ -210,15 +210,15 @@
acc
end).to eq({
"cytof_pool" => {
"pool-b" => {"restricted" => "false"},
"pool-d" => {"restricted" => "false"},
"pool-b" => {"restricted" => false},
"pool-d" => {"restricted" => false},
},
"sc_rna_seq_pool" => {
"pool-g" => {"restricted" => "false"},
"pool-j" => {"restricted" => "false"},
"pool-g" => {"restricted" => false},
"pool-j" => {"restricted" => false},
},
"patient" => {
"Danielle" => {"restricted" => "false"},
"Danielle" => {"restricted" => false},
}
})
end
Expand Down
10 changes: 7 additions & 3 deletions polyphemus/spec/spec_helper.rb
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Expand Up @@ -182,15 +182,15 @@ def stub_magma_all_pools(base_model, all_pools)
}.to_json })
end

def stub_magma_setup(patient_documents)
def stub_magma_setup(patient_documents, use_json: false)
stub_request(:post, "#{MAGMA_HOST}/retrieve")
.with(body: hash_including({ project_name: "mvir1", model_name: "patient",
attribute_names: ["name", "consent", "restricted"], record_names: "all" }))
.to_return({ body: {
'models': { 'patient': { 'documents': patient_documents } },
}.to_json })

stub_magma_update("mvir1")
use_json ? stub_magma_update_json : stub_magma_update("mvir1")
end

def stub_magma_update(project_name = nil)
Expand Down Expand Up @@ -344,7 +344,11 @@ def stub_magma_models(fixture: "spec/fixtures/magma_test_models.json")

def stub_magma_update_json
stub_request(:post, /#{MAGMA_HOST}\/update$/)
.to_return({ status: 200, body: {}.to_json, headers: { 'Content-Type': "application/json" } })
.to_return do |request|
params = JSON.parse(request.body)
@all_updates << params["revisions"] if @all_updates && params && params["revisions"]
{ body: "{}", status: 200, headers: { 'Content-Type': "application/json" } }
end
end

def stub_redcap_data(stub = nil)
Expand Down