use open3 cmd

dgidb · Dec 20, 2024 · 89dc9c1 · 89dc9c1
1 parent c67baed
commit 89dc9c1
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Showing 4 changed files with 13 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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