fixed pytest issues

ectyper/speciesIdentification.py

@@ -264,6 +264,7 @@ def verify_ecoli_and_inputs(fasta_fastq_files_dict, ofiles, filesnotfound, args)
     ecoli_files_dict = {}
     other_files_dict = {}
     filesnotfound_dict = {}
+    failverifyerrormessage = ''
 
     fasta_files = fasta_fastq_files_dict.keys()
 
@@ -279,7 +280,7 @@ def verify_ecoli_and_inputs(fasta_fastq_files_dict, ofiles, filesnotfound, args)
             raise ValueError(error_msg)
 
         if is_valid_fasta_file(fasta, sampleName) == False:
-            failverifyerrormessage = f"Sample {sampleName} FASTA file ({fasta}) is invalid/empty. This could happen when FASTA file generated from FASTQ input lacks raw reads mapping to O- and H- antigens database or input FASTA is empty/corrupted. Please check sequence input file of {sampleName}"
+            failverifyerrormessage += f"Sample {sampleName} FASTA file ({fasta}) is invalid/empty. This could happen when FASTA file generated from FASTQ input lacks raw reads mapping to O- and H- antigens or input FASTA is corrupted. Please check sequence input file '{sampleName}'."
 
 
         #do species always regardless of --verify param. Do prediction on fastq files if available for better accuracy
@@ -290,7 +291,7 @@ def verify_ecoli_and_inputs(fasta_fastq_files_dict, ofiles, filesnotfound, args)
             speciesname = get_species(fasta, args, args.cores)
 
         if args.verify:
-            failverifyerrormessage = "Sample identified as " + speciesname + ": serotyping results are only available for E.coli samples." \
+            failverifyerrormessage += "Sample identified as " + speciesname + ": serotyping results are only valid for E.coli samples." \
                                                                              "If sure that sample is E.coli run without --verify parameter."
             if re.match("Escherichia coli", speciesname):
                 ecoli_files_dict[sampleName] = {"species":speciesname,

test/test_complex_inputs.py

@@ -57,12 +57,12 @@ def test_emtpy_BLAST_antigen_hits(tmpdir):
 
 def test_invalid_fasta():
      fastafile=os.path.join(TEST_ROOT, 'Data/invalid_fasta.fasta')
-     set_input(input=fastafile, verify=False, refseqmash=True)
+     set_input(input=fastafile, verify=True, refseqmash=True)
      args = ectyper.commandLineOptions.parse_command_line()
      ecoli_files_dict, other_files_dict,filesnotfound_dict = ectyper.speciesIdentification.verify_ecoli_and_inputs(fasta_fastq_files_dict={fastafile:''}, ofiles=[], filesnotfound=[], args=args)
      assert ecoli_files_dict == {}
      assert other_files_dict['invalid_fasta']['error'] != ''
-     assert 'is empty' in other_files_dict['invalid_fasta']['error'], f'"is empty" not found in "{other_files_dict['invalid_fasta']['error']}"' 
+     assert 'is invalid/empty' in other_files_dict['invalid_fasta']['error'], f'"is invalid/empty" not found in "{other_files_dict['invalid_fasta']['error']}"' 
      assert filesnotfound_dict == {}
 
 

test/test_ectyper_integration.py

@@ -17,6 +17,7 @@ def set_input(input,
               percent_iden=None,
               verify = True,
               output=tempfile.mkdtemp(),
+              maxdirdepth=0,
               cores=1,
               print_sequence=False):
     """
@@ -27,7 +28,7 @@ def set_input(input,
     :return: None
     """
     args = ['-i', input,
-            #'-r', os.path.join(TEST_ROOT, 'Data/test_sketch.msh'),
+            '--maxdirdepth', str(maxdirdepth),
             '-c', str(cores)]
 
     if percent_iden:
@@ -134,10 +135,10 @@ def test_multiple_directories(caplog):
     :return: None
     """
     the_dir = os.path.join(TEST_ROOT, 'Data/test_dir')
-    set_input(the_dir, cores=4, verify=True, print_sequence=True)
+    set_input(the_dir, cores=4, verify=True, maxdirdepth=1, print_sequence=True)
     ectyper.run_program()
-    assert any([True if re.match(r".+sample2.+WARNING\s+\(WRONG\s+SPECIES\)", line) else False for line in caplog.text.splitlines()]), "Issue with sample2"
-    assert any([True if re.match(r".+sample3.+WARNING\s+\(WRONG\s+SPECIES\)", line) else False for line in caplog.text.splitlines()]), "Issue with sample3"
+    assert any([True if re.match(r".+sample2.+WARNING\s+\(WRONG\s+SPECIES\)", line) else False for line in caplog.text.splitlines()]), "Issue with sample 2"
+    assert any([True if re.match(r".+sample3.+WARNING\s+\(WRONG\s+SPECIES\)", line) else False for line in caplog.text.splitlines()]), "Issue with sample 3"
     assert any([True if re.match(r".+sample4.+WARNING\s+\(WRONG\s+SPECIES\)", line) else False for line in caplog.text.splitlines()]), "Issue with sample 4" 
     assert any([True if re.match(r".+badfasta.+WARNING\s+\(WRONG\s+SPECIES\).+Non fasta / fastq file", line) else False for line in caplog.text.splitlines()]), "Issue with badfasta"
     assert any([True if re.match(r".+sample.fasta.+WARNING\s+\(WRONG\s+SPECIES\).+Non fasta / fastq file", line) else False for line in caplog.text.splitlines()]), "Issue with sample.fasta"