fix(preprocessor): make search path precedence count

Create list directly without using set to retain input order information.
PharmGKB · Nov 12, 2024 · 1b5754d · 1b5754d
1 parent d2078f0
commit 1b5754d
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/preprocessor/pharmcat_pipeline b/preprocessor/pharmcat_pipeline
@@ -192,21 +192,20 @@ lead to different results.
         script_dir: Path = Path(globals().get("__file__", "./_")).absolute().parent
 
         # make sure we have pharmcat.jar
-        m_pharmcat_jar: Path = preprocessor.find_file(preprocessor.PHARMCAT_JAR_FILENAME, list({script_dir}))
+        m_pharmcat_jar: Path = preprocessor.find_file(preprocessor.PHARMCAT_JAR_FILENAME, [script_dir])
         if m_pharmcat_jar is None:
             print('Downloading %s...' % preprocessor.PHARMCAT_JAR_FILENAME)
             m_pharmcat_jar = preprocessor.download_pharmcat_jar(script_dir, verbose=args.verbose)
 
         # make sure we have pharmcat_positions.vcf.bgz
-        m_pharmcat_positions_vcf: Path = preprocessor.find_file(preprocessor.PHARMCAT_POSITIONS_FILENAME,
-                                                                list({script_dir}))
+        m_pharmcat_positions_vcf: Path = preprocessor.find_file(preprocessor.PHARMCAT_POSITIONS_FILENAME, [script_dir])
         if m_pharmcat_positions_vcf is None:
             print('Downloading %s...' % preprocessor.PHARMCAT_POSITIONS_FILENAME)
             m_pharmcat_positions_vcf = preprocessor.download_pharmcat_accessory_files(script_dir, verbose=args.verbose)
 
         # make sure we have reference FASTA
         m_reference_genome: Path = preprocessor.find_file(preprocessor.REFERENCE_FASTA_FILENAME,
-                                                          list({m_pharmcat_positions_vcf.parent, script_dir}))
+                                                          [m_pharmcat_positions_vcf.parent, script_dir])
         if m_reference_genome is None:
             print('Downloading reference FASTA.  This may take a while...')
             m_reference_genome = preprocessor.download_reference_fasta_and_index(m_pharmcat_positions_vcf.parent,

diff --git a/preprocessor/pharmcat_vcf_preprocessor.py b/preprocessor/pharmcat_vcf_preprocessor.py
@@ -141,7 +141,7 @@
             m_pharmcat_positions_vcf = preprocessor.validate_file(args.reference_pgx_vcf)
         else:
             m_pharmcat_positions_vcf = preprocessor.find_file(preprocessor.PHARMCAT_POSITIONS_FILENAME,
-                                                              list({Path.cwd(), script_dir}))
+                                                              [Path.cwd(), script_dir])
             if m_pharmcat_positions_vcf is None:
                 print('Downloading pharmcat_positions.vcf...')
                 m_pharmcat_positions_vcf = preprocessor.download_pharmcat_accessory_files(script_dir,
@@ -153,7 +153,7 @@
             m_reference_genome = preprocessor.validate_file(args.reference_genome)
         else:
             m_reference_genome = preprocessor.find_file(preprocessor.REFERENCE_FASTA_FILENAME,
-                                                        list({m_pharmcat_positions_vcf.parent, Path.cwd(), script_dir}))
+                                                        [m_pharmcat_positions_vcf.parent, Path.cwd(), script_dir])
             if m_reference_genome is None:
                 print('Downloading reference FASTA.  This may take a while...')
                 m_reference_genome = preprocessor.download_reference_fasta_and_index(m_pharmcat_positions_vcf.parent,