FI-3376 Migrate Evaluator CLI into inferno core CLI #557

jhlee-mitre · 2024-11-15T16:15:35Z

Summary

Since the evaluator requires a validator service and fhirpath service, it seems to make the most sense to have the evaluator be part of inferno core. Migrate the CLI class into inferno core such that it can be invoked with bundle exec inferno evaluate .....

This does not include any other integrations at this point - the IG does not need to be parsed, no rules need to run against the data, etc. However this may include or touch additional files needed to require everything, etc

Method

FHIR evaluator is added /dsl
FHIR evaluator codes are placed /dsl/fhir_evaluator Rule files are not added at this point to pass Rubocop.
Inferno CLI added evaluate method

All test cases passed and rubocop passed

Testing Guidance

To test, run command:

bundle exec inferno evaluate

Nothing actually happens but a message of execution confirmation.

codecov · 2024-11-15T16:18:55Z

Codecov Report

Attention: Patch coverage is 50.53763% with 46 lines in your changes missing coverage. Please review.

Project coverage is 84.17%. Comparing base (bcb8fb6) to head (796f383).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...b/inferno/dsl/fhir_evaluation/evaluation_result.rb	36.00%	16 Missing ⚠️
lib/inferno/dsl/fhir_evaluation/dataset_loader.rb	33.33%	12 Missing ⚠️
lib/inferno/dsl/fhir_evaluation/evaluator.rb	60.00%	8 Missing ⚠️
.../inferno/dsl/fhir_evaluation/evaluation_context.rb	58.33%	5 Missing ⚠️
lib/inferno/dsl/fhir_evaluation/config.rb	63.63%	4 Missing ⚠️
lib/inferno/dsl/fhir_evaluation/rule.rb	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #557      +/-   ##
==========================================
- Coverage   84.44%   84.17%   -0.28%     
==========================================
  Files         265      271       +6     
  Lines       11488    11581      +93     
  Branches     1266     1277      +11     
==========================================
+ Hits         9701     9748      +47     
- Misses       1777     1823      +46     
  Partials       10       10

Flag	Coverage Δ
backend	`92.58% <50.53%> (-0.93%)`	⬇️
frontend	`79.15% <ø> (ø)`

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dehall

Ok I think this is a good start for us. I suggest leaving a couple things out for now until we know they're needed. I also think for any nontrivial additions to core we need a review from @Jammjammjamm

dehall · 2024-11-18T16:43:27Z

lib/inferno/dsl/fhir_evaluator/ig.rb

+require 'rubygems/package'
+require 'zlib'
+
+module FhirEvaluator


I guess it doesn't hurt to leave this class in, but I thought migrating this over might be best left for the next step since we need to integrate with the validator, so the IG tgz will need to be in a specific folder. (Or we'll need to load from a package server)

I wonder where this will be migrated, do you think it will be part of Inferno utils?
Does Inferno have similar util already (extracting key contents from IGs) that can reuse to extend?

Good question. There's nothing in core that parses an IG that I'm aware of, but there are things in various test kits that this was inspired by, for example these in us-core-test-kit
https://github.com/inferno-framework/us-core-test-kit/blob/main/lib/us_core_test_kit/generator/ig_loader.rb
https://github.com/inferno-framework/us-core-test-kit/blob/main/lib/us_core_test_kit/generator/ig_resources.rb

I believe https://oncprojectracking.healthit.gov/support/browse/FI-3440 concerns this issue, which is next phase of the integration. I am okay to do it in this PR though it looks like phase 1 is already overwhelmed by many issues.

Yeah that's what I meant before - since we have a separate task for migrating this IG class and the class isn't used yet, it might be easier to just leave it out for now

lib/inferno/dsl/fhir_evaluation.rb

lib/inferno/dsl/fhir_evaluator/data_summary.rb

lib/inferno/dsl/fhir_evaluator/evaluator_util.rb

jhlee-mitre · 2024-11-19T13:20:12Z

Ok I think this is a good start for us. I suggest leaving a couple things out for now until we know they're needed. I also think for any nontrivial additions to core we need a review from @Jammjammjamm

Right, added him for review.

lib/inferno/apps/cli/main.rb

lib/inferno/dsl/fhir_evaluation.rb

Jammjammjamm · 2024-11-19T13:42:46Z

lib/inferno/dsl/fhir_evaluation.rb

+          end
+
+          require_relative 'fhir_evaluator/cli'
+          FhirEvaluator::CLI.start


The evaluator is expected to work both in and out of the CLI, so there should be no CLI-specific code inside inferno/dsl.

The evaluator CLI is removed.

Jammjammjamm · 2024-11-19T13:43:30Z

lib/inferno/dsl/fhir_evaluator/cli.rb

+require 'yaml'
+require 'pathname'
+
+module FhirEvaluator


I don't understand why this is separate from apps/cli/evaluator.

Everything in inferno needs to be inside the Inferno module. Anything inf inferno/dsl should be inside Inferno::DSL.

The evaluator CLI is removed and the evaluator is called from apps/cli/evaluator.

lib/inferno/dsl/fhir_evaluator/config.rb

lib/inferno/dsl/fhir_evaluator/evaluation_result.rb

lib/inferno/dsl/fhir_evaluator/evaluator.rb

lib/inferno/dsl/fhir_evaluator/version.rb

Jammjammjamm · 2024-11-19T14:14:13Z

lib/inferno/dsl/fhir_evaluator/rule.rb

+    end
+
+    # Get the subclasses of this class, ie, the actual implemented Rules.
+    def self.descendants


I think Class.descendants already exists and you shouldn't have to reimplement it.

You don't need the inherited hook either.

Jammjammjamm

The US Core IG should not be included. I also expect to see some unit tests.

Jammjammjamm · 2024-12-02T16:54:31Z

lib/inferno/dsl/fhir_evaluation.rb

+    module FHIREvaluation
+      class Evaluator
+        def initialize(ig_path, data_path)
+          Dotenv.load


This shouldn't have to deal with Dotenv. Inferno itself should handle that.

Jammjammjamm · 2024-12-02T16:54:52Z

lib/inferno/dsl/fhir_evaluation.rb

+module Inferno
+  module DSL
+    module FHIREvaluation
+      class Evaluator


This all seems like CLI-specific code that should belong in the CLI.

Based on conversation with Jaehoon - this file will be merged into the apps/cli/evaluator.rb file

Jammjammjamm · 2024-12-02T16:56:07Z

lib/inferno/dsl/fhir_evaluator/data_summary.rb

+module FhirEvaluator
+  # DataSummary represents the results of performing data characterization.
+  class DataSummary
+    attr_accessor :root_resource_ids, # All Example (root resource) Ids


All the comments are still there.

Jammjammjamm · 2024-12-02T16:57:25Z

lib/inferno/dsl/fhir_evaluator/data_summary.rb

+                  :resource_patient_map,  # Resources and corresponding Patient Ids as subject
+                  :resource_subject_map   # Resources and corresponding subject
+
+    def initialize(_data)


Why does this constructor have an unused argument? Is there a reason it isn't being stored in an instance variable so that it doesn't have to be passed around to various methods?

Per discussion with Dylan, we wll remove this file. The comment is archived at https://gitlab.mitre.org/inferno/fhir_evaluator/-/issues/1. We will come back to this when we decide to reuse.

Jammjammjamm · 2024-12-02T16:59:22Z

lib/inferno/dsl/fhir_evaluator/data_summary.rb

+      end
+    end
+
+    def to_json(*_args)


A method called to_json needs to return a json string. If you need a method which builds the hash which to_json stringifies, you can call it as_json.

Per discussion with Dylan, we wll remove this file. The comment is archived at https://gitlab.mitre.org/inferno/fhir_evaluator/-/issues/1. We will come back to this when we decide to reuse.

Jammjammjamm · 2024-12-02T17:08:41Z

lib/inferno/dsl/fhir_evaluator/ig.rb

+    attr_accessor :profiles, :extensions, :value_sets, :search_params, :examples
+
+    def initialize(ig_path)
+      raise "#{ig_path} is not an IG file" unless File.file?(ig_path)


This constructor is doing way too much. It shouldn't be doing much more than assigning instance variables. Make a class method that initializes the object and then performs the operations rather than having it all done in the constructor.

The file is deleted. IG import will be handled at phase 2.

Jammjammjamm · 2024-12-02T17:11:12Z

lib/inferno/dsl/fhir_evaluator/rules/abstract_has_examples_rule.rb

+
+module FhirEvaluator
+  module Rules
+    class HasExamples < Rule


This class name sounds like a module rather than a class. The filename needs to match the class/module name.

The file is deleted.

Jammjammjamm · 2024-12-02T17:15:45Z

lib/inferno/dsl/fhir_evaluator/data_summary.rb

@@ -0,0 +1,96 @@
+module FhirEvaluator


Anything inside Inferno needs to be inside the Inferno module. Anything in inferno/dsl needs to be inside Inferno::DSL.

The file is deleted.

Jammjammjamm · 2024-12-02T17:35:16Z

lib/inferno/dsl/fhir_evaluation.rb

+      class Evaluator
+        def initialize(ig_path, data_path)
+          Dotenv.load
+          Dir.glob(File.join(__dir__, 'fhir_evaluator', 'rules', '*.rb')).each do |file|


This should not be happening as part of the constructor. It should go with the other requires.

Commented out this part for now as we don't read rules at initial integration, will come back at phase 3.

Jammjammjamm · 2024-12-02T17:38:27Z

lib/inferno/dsl/fhir_evaluator/data_summary.rb

+      # @resource_subject_map = data.map { |e| resources_subjects(e) }.flatten.uniq
+    end
+
+    def extract_resources_ids(resource)


These extract_noun1_noun2 method names don't make sense to me. Is it extracting the first noun, the second noun, or both? They should be renamed.

Per discussion with Dylan, we wll remove this file. The comment is archived at https://gitlab.mitre.org/inferno/fhir_evaluator/-/issues/1. We will come back to this when we decide to reuse.

dehall · 2024-12-02T19:21:29Z

lib/inferno/dsl/fhir_evaluation.rb

+module Inferno
+  module DSL
+    module FHIREvaluation
+      class Evaluator


Based on conversation with Jaehoon - this file will be merged into the apps/cli/evaluator.rb file

dehall · 2024-12-02T19:29:30Z

lib/inferno/dsl/fhir_evaluator/config/default.yml

@@ -0,0 +1,80 @@
+# Common configuration.


From discussion - this file should be as empty as possible for the initial impl

Keep configurations only actively used.
Removed all Rule configurations for now as we don't run any rules for now.

dehall · 2024-12-02T19:31:54Z

lib/inferno/dsl/fhir_evaluator/data_summary.rb

@@ -0,0 +1,96 @@
+module FhirEvaluator


From discussion - delete this file

dehall · 2024-12-02T19:33:13Z

lib/inferno/dsl/fhir_evaluator/dataset.rb

+      # A Dataset returns an Array of FHIR data to be summarized or evaluated,
+      # with convenience methods for loading from a file path or from an
+      # Array of FHIR JSON strings.
+      module DatasetLoader


From discussion - update filename to match module name

dehall · 2024-12-02T19:38:59Z

lib/inferno/dsl/fhir_evaluator/evaluator_util.rb

@@ -0,0 +1,81 @@
+module Util


From discussion - delete this file but preserve Steve's comments in a GitLab issue for when we eventually bring this in

dehall · 2024-12-02T19:41:36Z

lib/inferno/dsl/fhir_evaluator/ig.rb

@@ -0,0 +1,89 @@
+# frozen_string_literal: true


From discussion - delete this file; it will be added back in FI-3440 as noted. I copied Steve's comment into that issue on Jira

dehall · 2024-12-02T19:43:15Z

lib/inferno/dsl/fhir_evaluator/rules/abstract_has_examples_rule.rb

@@ -0,0 +1,27 @@
+# frozen_string_literal: true


From discussion - delete this file, note Steve's comment

dehall · 2024-12-02T19:43:39Z

lib/inferno/dsl/fhir_evaluator/rules/all_defined_extensions_have_examples.rb

@@ -0,0 +1,44 @@
+# frozen_string_literal: true


From discussion - delete this file

dehall · 2024-12-02T19:44:58Z

lib/inferno/dsl/fhir_evaluator/ig/uscore7.0.0.tgz

From discussion - delete this file

dehall · 2024-12-06T12:03:55Z

lib/inferno/dsl/fhir_evaluator/evaluator.rb

+          context.results
+        end
+
+        def validate_args(ig_path, data_path)


I think we had a miscommunication somewhere - everything related to file paths and reading files should be in the CLI, in apps/cli/evaluator.rb . Apologies the file names are the same but I'm not sure what better unique names might be.

So pretty much everything in this file now except the evaluate method should be migrated over there. I think this file was good as of this earlier revision: https://github.com/inferno-framework/inferno-core/blob/5d1ef09fc3cfe428eb52ef0b5be0ec2f90e15f33/lib/inferno/dsl/fhir_evaluator/evaluator.rb

I believe you mentioned CLI can include actual logics to run the evaluator, but I missed it. I will move them over under CLI.

Speaking of file names, is the subfolder name dsl/fhir_evaluator good, or dsl/fhir_evaluation is even better?

Looking around other DSLs, they are like fhir_validation or fhirpath_evaluation. But some are like fhir_client_builder. Looks like some mix of ~on and ~er.

Sure I'm fine with changing names to make them more consistent with the rest of the system. Since the validator is module FHIRResourceValidation , class Validator , we would probably want this module to be FHIREvaluation and the DSL class to remain as Evaluator. If it helps distinguish things, maybe we want the cli class to be apps/cli/evaluate.rb instead of apps/cli/evalutator.rb?

Agreed. evaluate is more aligned with others e.g. execute.

dehall · 2024-12-09T16:59:28Z

lib/inferno/dsl/fhir_evaluator/config.rb

+
+          raise(TypeError, 'Malformed configuration') unless @data.is_a?(Hash)
+
+          # def method_missing(name, *args, &)


I assume the point of all this method_missing stuff and Section class was so that nested fields could be referenced as config.rule.rule_name.whatever instead of config['rule']['rule_name']['whatever']. If we don't want to do that anymore we should delete this rather than comment it out. Or if we do want to support that, uncomment this. I feel like it's nice but not necessary

I think it is good to have in the end, but we discussed config.yml to have it simple at this phase and I removed all Rule related configurations. So for now we aren't using this as there's no configuration to call. I will remove this and come back to this if we have clear picture of config later.

lib/inferno/dsl/fhir_evaluator/evaluator.rb

dehall · 2024-12-09T17:26:15Z

lib/inferno/dsl/fhir_evaluator/evaluator.rb

+      class Evaluator
+        attr_accessor :data, :config
+
+        def initialize(data, config)


I haven't kept up with all of @Jammjammjamm 's comments so I hope I'm not suggesting a reversion of one of them here, but the method signatures in this class are kind of reversed from how they originally were in the gitlab repo:

def initialize(the_ig) @ig = the_ig end def evaluate(data, summary = nil, config = Config.new)

At minimum the ig param will need to be added back in somewhere.

But the way I originally envisioned this is that one could theoretically create one evaluator per IG, and then call evaluate on multiple sets of data. As it is now I guess I don't see the benefit of the constructor and the attr_accessors, everything is pretty contained in the evaluate method.

I actually removed the IG part while refactoring evaluator as you took over the IG task and expected to handle whatever about IG. I will put IG attr_accessors back in constructor.

If the evaluator is designed to use for one IG with multiple data, Yes, data shouldn't be attr_accessors. About Config, for now it is fixed and universal for all data, but we only have minimum (almost empty) there. I will put it under evaluate as you suggested.

Co-authored-by: Dylan Hall <dehall@mitre.org>

Jammjammjamm · 2024-12-10T16:26:53Z

lib/inferno/dsl/fhir_evaluator/config/default.yml

@@ -0,0 +1,9 @@
+Environment:


I definitely don't think we should have a folder just for this one file. Is there a bunch of stuff that will be added to it? I don't see much value in this file as is.

Originally config yml was assumed to include list of rules and their individual configurations, which brings possibilities of large ymls with customizations depending on use cases of the evaluator. We don't have clear picture of what it will be. Dylan's suggestion is to make it simplest at this phase. I agree with you that it doesn't have much value as it is.

Jammjammjamm · 2024-12-10T16:27:46Z

lib/inferno/dsl/fhir_evaluator/dataset_loader.rb

+            dataset.push resource
+          end
+
+          puts "Loaded #{dataset.length} resources"


We shouldn't have print statements outside of the CLI.

Removed all print statements. Will come back when we have logger for the evaluator.

Jammjammjamm · 2024-12-10T16:27:57Z

lib/inferno/dsl/fhir_evaluator/dataset_loader.rb

+module Inferno
+  module DSL
+    module FHIREvaluation
+      # A Dataset returns an Array of FHIR data to be summarized or evaluated,


This comment is out of date.

Jammjammjamm · 2024-12-10T16:28:45Z

lib/inferno/dsl/fhir_evaluator/evaluation_context.rb

+      class EvaluationContext
+        attr_reader :ig, :data, :results, :config
+
+        def initialize(the_ig, data, config)


I don't see why the_ig isn't just named ig.

It's because there's a rubocop complaint if we use just ig unfortunately:

lib/inferno/dsl/fhir_evaluator/evaluation_context.rb:12:24: C: Naming/MethodParameterName: Method parameter must be at least 3 characters long. def initialize(ig, data, config)

Oh, right. It doesn't pass Rubocop with ig

This is definitely a case where you should disable that rule for this line.

Jammjammjamm · 2024-12-10T18:06:40Z

lib/inferno/dsl/fhir_evaluator/evaluator.rb

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+require 'dotenv'


I don't know that any of these requires are necessary.

Jammjammjamm · 2024-12-10T18:12:15Z

lib/inferno/dsl/fhir_evaluator/config.rb

@@ -0,0 +1,21 @@
+module Inferno
+  module DSL
+    module FHIREvaluation


The module name and the file path don't match.

Jammjammjamm · 2024-12-12T12:58:51Z

lib/inferno/dsl/fhir_evaluation/evaluation_context.rb

+      class EvaluationContext
+        attr_reader :ig, :data, :results, :config
+
+        # rubocop:disable Naming/MethodParameterName


Instead of using a disable and an enable, just put the disable at the end of the relevant line, and then it will only affect that line and you don't have to reenable the rule.

Thanks for the tips. Modified.

Copied evaluator files

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jhlee-mitre and others added 4 commits November 15, 2024 11:22

Rubocop

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Robocop

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Rubocop temporarily addressed

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Merge branch 'main' into FI-3376-evaluator-firststep

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jhlee-mitre requested a review from dehall November 15, 2024 20:01

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Remove old comment

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Removed internal valiadator method

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Leave out DataSummary

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jhlee-mitre self-assigned this Nov 21, 2024

jhlee-mitre added 11 commits November 21, 2024 08:37

Remove evaluator version

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Long description

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rubocop

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WIP

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WIP

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Data set loader

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IG path resolved

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WIP

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WIP

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rubocop

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Rubocop

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jhlee-mitre requested review from Jammjammjamm and dehall December 2, 2024 15:37

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jhlee-mitre added 3 commits December 5, 2024 22:52

WIP

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Clean up

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config

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dehall reviewed Dec 6, 2024

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jhlee-mitre added 2 commits December 6, 2024 19:19

Rename evaluator

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Args

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jhlee-mitre marked this pull request as ready for review December 9, 2024 13:41

jhlee-mitre requested review from Jammjammjamm and dehall December 9, 2024 13:42

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lib/inferno/dsl/fhir_evaluator/evaluator.rb Outdated Show resolved Hide resolved

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jhlee-mitre and others added 3 commits December 10, 2024 08:24

Update lib/inferno/dsl/fhir_evaluator/evaluator.rb

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Co-authored-by: Dylan Hall <dehall@mitre.org>

ig initialize, missing_method

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Merge branch 'main' into FI-3376-evaluator-firststep

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the_ig

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Disable rubocop for IG

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Remove print

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Folder file names

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Removed config folder

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jhlee-mitre requested review from Jammjammjamm and dehall December 11, 2024 15:45

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jhlee-mitre and others added 2 commits December 12, 2024 08:12

rubocop:disable Naming/MethodParameterName

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Merge branch 'main' into FI-3376-evaluator-firststep

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jhlee-mitre merged commit 4034350 into main Dec 12, 2024
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dehall deleted the FI-3376-evaluator-firststep branch December 12, 2024 16:39

jhlee-mitre mentioned this pull request Jan 3, 2025

FI-3441 Migrate Evaluator rules to Inferno core [1 of 4] #583

Open


		raise(TypeError, 'Malformed configuration') unless @data.is_a?(Hash)

		# def method_missing(name, *args, &)

		@@ -0,0 +1,44 @@
		# frozen_string_literal: true

		require 'dotenv'

FI-3376 Migrate Evaluator CLI into inferno core CLI #557

FI-3376 Migrate Evaluator CLI into inferno core CLI #557

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jhlee-mitre commented Nov 15, 2024 •

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