Added test of no directory specified and testing for multiple files i…

…nputs. Added solution to issue #87

ectyper/ectyper.py

@@ -276,6 +276,7 @@ def create_output_directory(args):
             str(datetime.datetime.now().time()).replace(':', '.')
         ])
         out_dir = os.path.join(definitions.WORKPLACE_DIR, date_dir)
+        LOG.info(f"No output folder specified .... All output will be saved in {out_dir}")
         args.output = out_dir
     else:
         if os.path.isabs(args.output):

ectyper/subprocess_util.py

@@ -2,7 +2,7 @@
 
 import logging
 import subprocess
-import timeit
+import timeit, os
 
 LOG = logging.getLogger(__name__)
 
@@ -17,7 +17,8 @@ def run_subprocess(cmd, input_data=None, un=False, ignorereturncode=False):
     Returns:
         stdout (str): The stdout of cmd
     """
-
+    env_copy = os.environ.copy()
+    env_copy['LC_ALL'] = "C" #issue 87 to get consistent sorting (https://github.com/phac-nml/ecoli_serotyping/issues/87)
     start_time = timeit.default_timer()
     comp_proc = subprocess.run(
         cmd,
@@ -26,7 +27,8 @@ def run_subprocess(cmd, input_data=None, un=False, ignorereturncode=False):
         check=False,
         universal_newlines=un,
         stdout=subprocess.PIPE,
-        stderr=subprocess.PIPE
+        stderr=subprocess.PIPE,
+        env=env_copy 
     )
 
 

test/test_complex_inputs.py

@@ -1,8 +1,8 @@
 import sys
 import pytest
 import tempfile
-import os, json
-from ectyper import ectyper
+import os, json, logging
+from ectyper import ectyper, commandLineOptions
 
 
 
@@ -66,4 +66,33 @@ def test_invalid_fasta():
      assert filesnotfound_dict == {}
 
 
+def test_no_output_dir_specified():  
+    fastafile=os.path.join(TEST_ROOT, 'Data/Escherichia.fna')
+    set_input(input=fastafile, output=None) 
+    args = commandLineOptions.parse_command_line()
+    output_directory = ectyper.create_output_directory(args)
+    print (output_directory)
+    assert 'ectyper_' in output_directory, "The output directory does not contain 'ectyper_' pattern"
+    assert os.path.exists(output_directory), f"{output_directory} does not exist"
+
+def test_multiple_inputs(caplog):
+    caplog.set_level(logging.DEBUG)
+    fastafiles=",".join([os.path.join(TEST_ROOT, 'Data/EscherichiaO17H18.fasta'),
+                        os.path.join(TEST_ROOT, 'Data/EscherichiaO28H5.fasta')])
 
+
+    set_input(input=fastafiles, output=os.path.join(TEST_ROOT,"ectyper_multiple_comma_inputs")) 
+    args = commandLineOptions.parse_command_line()
+    ectyper.run_program()
+    output_tsv = os.path.join(args.output,"output.tsv")
+    output_blastn_antigens = os.path.join(args.output,"blastn_output_alleles.txt")
+    assert os.path.exists(output_tsv), f"File missing {output_tsv}"
+    with open(output_tsv) as fp:
+        output_tsv_lines = fp.readlines()
+    with open(output_blastn_antigens) as fp:
+        output_blastn_antigens_lines  = fp.readlines()   
+    assert any([True if 'O17/O77/O44/O106:H18' in line else False for line in output_tsv_lines]), "No matches of 'O17/O77/O44/O106:H18' serotype"
+    assert any([True if 'O28/O42:H25' in line else False for line in output_tsv_lines]), "No matches of 'O28/O42:H25' serotype"
+    assert any([True if 'EscherichiaO17H18' in line else False for line in output_blastn_antigens_lines]), "No matches of 'EscherichiaO17H18' in BLAST output"
+    assert any([True if 'EscherichiaO28H5' in line else False for line in output_blastn_antigens_lines]), "No matches of 'EscherichiaO28H5' in BLAST output"
+

test/test_ectyper_speciesID.py

@@ -55,7 +55,6 @@ def test_failed_species_identification_nospeciesverify(caplog):
     file = os.path.join(TEST_ROOT, 'Data/GCF_001672015.1.fna')
     set_input(input=file, verify=False)
     ectyper.run_program()
-    print()
     assert "GCF_001672015.1\tEscherichia coli\t-\tH8\t-:H8\t-" in caplog.text