diff --git a/scripts/requirements.txt b/scripts/requirements.txt index a0aacec2..c593b402 100644 --- a/scripts/requirements.txt +++ b/scripts/requirements.txt @@ -3,6 +3,7 @@ boto3==1.35.84 botocore==1.35.84 certifi==2024.12.14 charset-normalizer==3.4.0 +click==8.1.7 decorator==5.1.1 executing==2.1.0 idna==3.10 @@ -27,5 +28,5 @@ tqdm==4.67.1 traitlets==5.14.3 typing_extensions==4.12.2 urllib3==2.2.3 -wags_tails==0.2.1 +wags_tails==0.2.2 wcwidth==0.2.13 diff --git a/server/lib/genome/importers/base.rb b/server/lib/genome/importers/base.rb index ca6dca66..6c1f2d4c 100644 --- a/server/lib/genome/importers/base.rb +++ b/server/lib/genome/importers/base.rb @@ -1,4 +1,5 @@ require 'csv' +require 'open3' module Genome module Importers @@ -41,7 +42,14 @@ def default_filename end def default_data_dir - "#{Dir.home}/.local/share/wags_tails" + begin + stdout, stderr, process_status = Open3.capture3('wags-tails path') + rescue Errno::ENOENT + raise 'wags-tails executable not found. Is it on your $PATH? See README.' + end + raise "wags-tails path lookup failed with code #{stderr}." unless process_status.success? + + stdout.chomp end def handle_file_location(file_path) diff --git a/server/lib/genome/importers/file_importers/clearity_foundation_biomarkers.rb b/server/lib/genome/importers/file_importers/clearity_foundation_biomarkers.rb index 09473534..f4b2de40 100644 --- a/server/lib/genome/importers/file_importers/clearity_foundation_biomarkers.rb +++ b/server/lib/genome/importers/file_importers/clearity_foundation_biomarkers.rb @@ -34,7 +34,7 @@ def create_new_source def handle_file_location(file_path) return file_path unless file_path.nil? - "#{Dir.home}/.local/share/wags_tails/clearity_foundation/clearity_foundation_biomarkers_claims.tsv" + "#{default_data_dir}/clearity_foundation/clearity_foundation_biomarkers_claims.tsv" end def create_interaction_claims diff --git a/server/lib/genome/importers/file_importers/clearity_foundation_clinical_trial.rb b/server/lib/genome/importers/file_importers/clearity_foundation_clinical_trial.rb index 19e8f5b5..194b7929 100644 --- a/server/lib/genome/importers/file_importers/clearity_foundation_clinical_trial.rb +++ b/server/lib/genome/importers/file_importers/clearity_foundation_clinical_trial.rb @@ -34,7 +34,7 @@ def create_new_source def handle_file_location(file_path) return file_path unless file_path.nil? - "#{Dir.home}/.local/share/wags_tails/clearity_foundation/clearity_foundation_clinical_trial_claims.tsv" + "#{default_data_dir}/clearity_foundation/clearity_foundation_clinical_trial_claims.tsv" end def create_interaction_claims