add install to every command in case

gbouras13 · Feb 23, 2024 · 1259f23 · 1259f23
1 parent 461ec48
commit 1259f23
Showing 1 changed file with 20 additions and 4 deletions.
diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -56,8 +56,6 @@ def remove_directory(dir_path):
 #     return tmpdir_factory.mktemp("tmp")
 
 
-temp_dir = Path(f"{test_data}/fake_out")
-
 # the server can be down
 run_remote = False
 
@@ -88,55 +86,71 @@ def test_install():
 def test_run_genbank():
     """test phold run with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold run -i {input_gbk} -o {run_gbk_dir} -t {threads}  --cpu -d {database_dir} -f"
     exec_command(cmd)
 
 
 def test_predict_genbank():
     """test phold predict with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold predict -i {input_gbk} -o {predict_gbk_dir} -t {threads}  --cpu -d {database_dir} -f"
     exec_command(cmd)
 
 
 def test_compare_genbank():
     """test phold compare with genbank input"""
     input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold compare -i {input_gbk} -o {compare_gbk_dir} --predictions_dir {predict_gbk_dir} -t {threads} -d {database_dir} -f"
     exec_command(cmd)
 
 
 def test_compare_pdb():
     """test phold compare with pdbs input"""
     input_gbk: Path = f"{test_data}/NC_043029.gbk"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold compare -i {input_gbk} -o {compare_pdb_dir} -t {threads} -d {database_dir} --pdb --pdb_dir {pdb_dir} -f"
     exec_command(cmd)
 
 
 def test_predict_fasta():
     """test phold predict with fasta input"""
     input_fasta: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold predict -i {input_fasta} -o {predict_fasta_dir} -t {threads} -d {database_dir}  --cpu -f"
     exec_command(cmd)
 
 
 def test_compare_fasta():
     """test phold compare with fasta input"""
     input_fasta: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.fasta"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold compare -i {input_fasta} -o {compare_fasta_dir} --predictions_dir {predict_fasta_dir} -t {threads} -d {database_dir} -f"
     exec_command(cmd)
 
 
 def test_proteins_predict():
     """test phold proteins-predict"""
     input_fasta: Path = f"{test_data}/phanotate.faa"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold proteins-predict -i {input_fasta} -o {proteins_predict_dir} -t {threads} -d {database_dir} --cpu -f"
     exec_command(cmd)
 
 
 def test_proteins_compare():
     """test phold proteins-compare"""
     input_fasta: Path = f"{test_data}/phanotate.faa"
+    cmd = f"phold install -d {database_dir} "
+    exec_command(cmd)
     cmd = f"phold proteins-compare -i {input_fasta} --predictions_dir {proteins_predict_dir} -o {proteins_compare_dir} -t {threads} -d {database_dir} -f"
     exec_command(cmd)
 
@@ -146,6 +160,8 @@ def test_proteins_compare():
     def test_remote_genbank():
         """test phold remote with genbank input"""
         input_gbk: Path = f"{test_data}/combined_truncated_acr_defense_vfdb_card.gbk"
+        cmd = f"phold install -d {database_dir} "
+        exec_command(cmd)
         cmd = f"phold remote -i {input_gbk} -o {remote_gbk_dir} -t {threads} -d {database_dir} -f"
         exec_command(cmd)
 
@@ -154,6 +170,8 @@ def test_remote_fasta():
         input_fasta: Path = (
             f"{test_data}/combined_truncated_acr_defense_vfdb_card.fasta"
         )
+        cmd = f"phold install -d {database_dir} "
+        exec_command(cmd)
         cmd = f"phold remote -i {input_fasta} -o {remote_fasta_dir} -t {threads} -d {database_dir} -f"
         exec_command(cmd)
 
@@ -170,5 +188,3 @@ def test_remote_fasta():
 
 
 remove_directory(output_dir)
-
-