etna 0.1.22 → 0.1.23

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3c3726db5513bc41e2909cbf25597ad3c83b3cb50c599fbf3f37e3efde11d47f
-  data.tar.gz: 8635c884833e3f403335c94f183609c6613e825964279dce349e145050eac0c1
+  metadata.gz: 6ae7868eeaa6de2a8701602929e642d381ccab2115c71cb18c216a362217645c
+  data.tar.gz: 9183c39484f21c330f1c0e14f4c9e355e8302805f71dbdbb5889f1e3eeb58bb4
 SHA512:
-  metadata.gz: 5d19841e9c12cca76030dfde0322c9e6e221d8799c13088bee0897db18acba38c04e1ae6841db8a04766136639f5a445cc286114e77f0747ab405c0f8aca0652
-  data.tar.gz: cff82b91e49e07100d7350444b034abccfbfa2e28e6e6cc9928097dd7317c263f4870dc6eca0164451f0759b12a358d7db13d441e8ebe9c2c1b0e287b684ce73
+  metadata.gz: 20ae9fdf11e4da6e000be9308e5c3f8b5309d219aa5820b4a855ee43b80d2f4c6bc7f33e52e1844ab3bfe02ee67968cbb91f53737a0a6515ba870b08dffe854e
+  data.tar.gz: a43573a1a801e9d4be0aee3390997b68507b6bdcb626fc185264eb8cb884b7e14d92a4485df5ec494527bd8609d761a7f7e1ca5c9064181789506e756f8d4157

data/etna.completion

@@ -136,7 +136,7 @@ all_flag_completion_names="$all_flag_completion_names  "
 string_flag_completion_names="$string_flag_completion_names  "
 while [[ "$#" != "0" ]]; do
 if [[ "$#" == "1" ]];  then
-all_completion_names="create_file_linking_csv help update_from_csv"
+all_completion_names="create_file_linking_csv help load_table_from_csv update_from_csv"
 all_completion_names="$all_completion_names $all_flag_completion_names"
 if [[ -z "$(echo $all_completion_names | xargs)" ]]; then
 return
@@ -252,6 +252,68 @@ return
 fi
 done
 return
+elif [[ "$1" == "load_table_from_csv" ]]; then
+shift
+if [[ "$#" == "1" ]];  then
+all_completion_names="__project_name__"
+if [[ -z "$(echo $all_completion_names | xargs)" ]]; then
+return
+fi
+COMPREPLY=($(compgen -W "$all_completion_names" -- "$1"))
+return
+fi
+shift
+if [[ "$#" == "1" ]];  then
+all_completion_names="__model_name__"
+if [[ -z "$(echo $all_completion_names | xargs)" ]]; then
+return
+fi
+COMPREPLY=($(compgen -W "$all_completion_names" -- "$1"))
+return
+fi
+shift
+if [[ "$#" == "1" ]];  then
+all_completion_names="__file_path__"
+if [[ -z "$(echo $all_completion_names | xargs)" ]]; then
+return
+fi
+COMPREPLY=($(compgen -W "$all_completion_names" -- "$1"))
+return
+fi
+shift
+all_flag_completion_names="$all_flag_completion_names --execute "
+string_flag_completion_names="$string_flag_completion_names  "
+while [[ "$#" != "0" ]]; do
+if [[ "$#" == "1" ]];  then
+all_completion_names=""
+all_completion_names="$all_completion_names $all_flag_completion_names"
+if [[ -z "$(echo $all_completion_names | xargs)" ]]; then
+return
+fi
+COMPREPLY=($(compgen -W "$all_completion_names" -- "$1"))
+return
+elif [[ -z "$(echo $all_flag_completion_names | xargs)" ]]; then
+return
+elif [[ "$all_flag_completion_names" =~ $1\  ]]; then
+all_flag_completion_names="${all_flag_completion_names//$1\ /}"
+a=$1
+shift
+if [[ "$string_flag_completion_names" =~ $a\  ]]; then
+if [[ "$#" == "1" ]];  then
+a="${a//--/}"
+a="${a//-/_}"
+i="_completions_for_$a"
+all_completion_names="${!i}"
+COMPREPLY=($(compgen -W "$all_completion_names" -- "$1"))
+return
+fi
+shift
+fi
+else
+return
+fi
+done
+return
 elif [[ "$1" == "update_from_csv" ]]; then
 shift
 if [[ "$#" == "1" ]];  then

data/lib/commands.rb

@@ -54,15 +54,16 @@ class EtnaApp
       boolean_flags << '--ignore-ssl'
 
       def execute(host, ignore_ssl: false)
-        polyphemus_client ||= Etna::Clients::Polyphemus.new(
+        polyphemus_client = Etna::Clients::Polyphemus.new(
             host: host,
             token: token(ignore_environment: true),
+            persistent: false,
             ignore_ssl: ignore_ssl)
         workflow = Etna::Clients::Polyphemus::SetConfigurationWorkflow.new(
             polyphemus_client: polyphemus_client,
             config_file: EtnaApp.config_file_path)
         config = workflow.update_configuration_file(ignore_ssl: ignore_ssl)
-        logger.info("Updated #{config.environment} configuration from #{host}.")
+        logger&.info("Updated #{config.environment} configuration from #{host}.")
       end
 
       def setup(config)
@@ -299,6 +300,49 @@ class EtnaApp
             workflow.write_csv_io(filename: file)
           end
         end
+
+        class LoadTableFromCsv < Etna::Command
+          include WithEtnaClients
+
+          boolean_flags << '--execute'
+
+          def execute(project_name, model_name, file_path, execute: false)
+            request = Etna::Clients::Magma::RetrievalRequest.new(project_name: project_name)
+            request.model_name = model_name
+            request.attribute_names = 'all'
+            request.record_names = 'all'
+            model = magma_client.retrieve(request).models.model(model_name)
+            model_parent_name = model.template.attributes.all.select do |attribute|
+              attribute.attribute_type == Etna::Clients::Magma::AttributeType::PARENT
+            end.first.name
+
+            other_attribute_names = model.template.attributes.all.reject do |attribute|
+              attribute.attribute_type == Etna::Clients::Magma::AttributeType::PARENT
+            end.map do |attribute|
+              attribute.name
+            end
+
+            # NOTE: This does not call ensure_parent currently because of MVIR1 consent--
+            #   if the timepoint doesn't exist, the patient may be no study? (one example, at least)
+            update_request = Etna::Clients::Magma::UpdateRequest.new(project_name: project_name)
+
+            data = CSV.parse(File.read(file_path), headers: true)
+
+            data.by_row.each do |row|
+              revision = {}
+              other_attribute_names.each do |attribute_name|
+                revision[attribute_name] = row[attribute_name] unless row[attribute_name].nil?
+              end
+              update_request.append_table(model_parent_name, row[model_parent_name], model_name, revision)
+            end
+
+            puts update_request
+
+            if execute
+              magma_client.update_json(update_request)
+            end
+          end
+        end
       end
     end
   end

data/lib/etna/spec/vcr.rb

@@ -30,6 +30,8 @@ def setup_base_vcr(spec_helper_dir)
       end
     end
 
+    # c.debug_logger = File.open('log/vcr_debug.log', 'w')
+
     c.default_cassette_options = {
         serialize_with: :compressed,
         record: if ENV['IS_CI'] == '1'
@@ -82,6 +84,11 @@ def setup_base_vcr(spec_helper_dir)
       end
     end
   end
+
+  require 'multipartable'
+  def Multipartable.secure_boundary
+    "--THIS-IS-STABLE-FOR-TESTING"
+  end
 end
 
 def prepare_vcr_secret

data/lib/helpers.rb

@@ -6,6 +6,15 @@ module WithEtnaClients
     EtnaApp.instance.environment
   end
 
+  def exit(status=true)
+    WithEtnaClients.exit(status)
+  end
+
+  # Abstraction used to prevent accidental exist in specs.
+  def self.exit(status)
+    Kernel.exit(status)
+  end
+
   def token(ignore_environment: false)
     unless ignore_environment
       if environment == :many

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: etna
 version: !ruby/object:Gem::Version
-  version: 0.1.22
+  version: 0.1.23
 platform: ruby
 authors:
 - Saurabh Asthana
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-12-15 00:00:00.000000000 Z
+date: 2020-12-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rack
@@ -117,6 +117,7 @@ files:
 - lib/etna/clients/magma/workflows/file_linking_workflow.rb
 - lib/etna/clients/magma/workflows/json_converters.rb
 - lib/etna/clients/magma/workflows/json_validators.rb
+- lib/etna/clients/magma/workflows/materialize_magma_record_files_workflow.rb
 - lib/etna/clients/magma/workflows/model_synchronization_workflow.rb
 - lib/etna/clients/magma/workflows/record_synchronization_workflow.rb
 - lib/etna/clients/magma/workflows/update_attributes_from_csv_workflow.rb