new dev-test sub branch for functional tests

functional_tests/functional_tests.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Usage
+    ## python 01_clean_qc.py -w [root directory of metagwgs source folder] [optional: --skip_nextflow]
+
+try:
+    import argparse
+    import sys
+    import re
+    import os
+    import os.path
+    import subprocess
+    import filecmp
+
+except ImportError as error:
+    print(error)
+    exit(1)
+
+# Lists of output files to compare
+
+_01_1_cleaned_reads = [
+    ("01_1_cleaned_reads/logs/a.no_filter.flagstat", "diff"),
+    ("01_1_cleaned_reads/logs/a_cutadapt.log", "cut_diff"),
+    ("01_1_cleaned_reads/logs/a_sickle.log", "diff"),
+    ("01_1_cleaned_reads/logs/host_filter_flagstat/a.host_filter.flagstat", "diff"),
+    ("01_1_cleaned_reads/logs/c.no_filter.flagstat", "diff"),
+    ("01_1_cleaned_reads/logs/c_cutadapt.log", "cut_diff"),
+    ("01_1_cleaned_reads/logs/c_sickle.log", "diff"),
+    ("01_1_cleaned_reads/logs/host_filter_flagstat/c.host_filter.flagstat", "diff")
+]
+
+_01_2_qc = [
+    ("01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R1_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R1_fastqc.zip", "not_empty"),
+    ("01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R2_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_cleaned/cleaned_a/cleaned_a_R1_fastqc.zip", "not_empty"),
+    ("01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R1_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R1_fastqc.zip", "not_empty"),
+    ("01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R2_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_cleaned/cleaned_c/cleaned_c_R1_fastqc.zip", "not_empty"),
+    ("01_2_qc/fastqc_raw/a/a_R1_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_raw/a/a_R1_fastqc.zip", "not_empty"),
+    ("01_2_qc/fastqc_raw/a/a_R2_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_raw/a/a_R2_fastqc.zip", "not_empty"),
+    ("01_2_qc/fastqc_raw/c/c_R1_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_raw/c/c_R1_fastqc.zip", "not_empty"),
+    ("01_2_qc/fastqc_raw/c/c_R2_fastqc.html", "not_empty"),
+    ("01_2_qc/fastqc_raw/c/c_R2_fastqc.zip", "not_empty")
+]
+
+_01_3_taxonomic_affiliation_reads = [
+    ("01_3_taxonomic_affiliation_reads/a.krona.html", "not_empty"),
+    ("01_3_taxonomic_affiliation_reads/c.krona.html", "not_empty"),
+    ("01_3_taxonomic_affiliation_reads/taxo_affi_reads_class.tsv", "diff"),
+    ("01_3_taxonomic_affiliation_reads/taxo_affi_reads_family.tsv", "diff"),
+    ("01_3_taxonomic_affiliation_reads/taxo_affi_reads_genus.tsv", "diff"),
+    ("01_3_taxonomic_affiliation_reads/taxo_affi_reads_order.tsv", "diff"),
+    ("01_3_taxonomic_affiliation_reads/taxo_affi_reads_phylum.tsv", "diff"),
+    ("01_3_taxonomic_affiliation_reads/taxo_affi_reads_species.tsv", "diff")
+]
+
+# List of steps:
+
+steps_list = [
+    "01_clean_qc",
+    "02",
+    "03",
+    "04",
+    "05",
+    "06",
+    "07",
+    "08"
+]
+
+# Arguments parsing (3 required / 1 optional)
+## Usage example:
+# 
+# python functional_tests.py \
+#   -step 01_clean_qc \
+#   -exp_dir ../../functional_tests/expected \
+#   -obs_dir ../../functional_tests/observed/results \
+#   --script ../../functional_tests/test.sh
+def parse_arguments():
+
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("-step", type = str, \
+    help = "(at least one required) step(s) of metagwgs you wish to perform a test on (multiple steps can be tested at once)")
+    parser.add_argument("-exp_dir", type = str, \
+    help = "(required) expected logs dir containing logs from a healthy metagwgs workflow")
+    parser.add_argument("-obs_dir", type = str, \
+    help = "(required) observed logs dir containing logs from the metagwgs workflow you wish to test")
+    parser.add_argument("--script", type = str, \
+    help = "(optional) script file containing metagwgs Nextflow launch command ")
+
+    if len(sys.argv) == 1:
+
+        parser.print_usage(sys.stderr)
+        sys.exit(1)
+
+    return parser.parse_args()
+
+# Launch nextflow from script if given by user
+def launch_nextflow(script):
+
+    script_file = os.path.abspath(script)
+    script_dir = os.path.dirname(script_file)
+
+    print("Launching test run with the provided file:\n\n{}\n".format(script_file))
+
+    process = subprocess.Popen(["sbatch", "{}".format(script_file)], cwd = script_dir, stdout = subprocess.PIPE, shell=True, executable = '/bin/bash')
+    output, error = process.communicate()
+
+    print("Test run completed")
+
+# Do file comparisons for 01_clean_qc step and write output
+def check_01_clean_qc(files_list):
+
+    f = open("ft_01_clean_qc.log", "w+")
+
+    expected_prefix = "{}/01_clean_qc/".format(os.path.abspath(args.exp_dir))
+    observed_prefix = "{}/01_clean_qc/".format(os.path.abspath(args.obs_dir))
+
+    f.write("Expected directory: {}\nObserved directory: {}\n".format(expected_prefix, observed_prefix))
+
+    max_cnt = len(files_list)
+    true_cnt = 0
+    false_cnt = 0
+
+    print("\nLaunching 01_clean_qc...\n")
+
+    for file in files_list:
+
+        file_path = file[0]
+        file_usage = file[1]
+        
+        expected_path = "{}{}".format(expected_prefix, file_path)
+        observed_path = "{}{}".format(observed_prefix, file_path)
+
+        out = """
+------------------------------------------------------------------------------
+
+Path:       {}
+Test type:  {}
+
+""".format(file_path, file_usage)
+
+        f.write(out)
+        print(out)
+
+        if not os.path.exists("{}".format(expected_path)) or not os.path.exists("{}".format(observed_path)):
+
+            # Make log of non existing files
+            if not os.path.exists("{}".format(expected_path)):
+
+                sys.exit(
+                    "\n{} doesn't exist\n\nPlease check expected/ directory for any missing file\n".format(expected_path)
+                )
+
+            elif not os.path.exists("{}".format(observed_path)):
+
+                sys.exit(
+                    "\n{} doesn't exist\n\nPlease check observed/ directory for any missing file\n".format(observed_path)
+                )
+
+        else:
+            
+            if file_usage == "diff":
+
+                test = filecmp.cmp(expected_path, observed_path)
+
+                if test:
+                    true_cnt += 1
+                else:
+                    false_cnt += 1
+
+                out = "Test result: {}\n".format(str(test))
+                f.write(out)
+                print(out)
+
+            elif file_usage == "cut_diff":
+
+                # Specifically remove header from cutadapt
+
+                command = "diff <(tail -n+6 {}) <(tail -n+6 {})".format(expected_path, observed_path)
+                process = subprocess.Popen(command, stdout = subprocess.PIPE, shell = True, executable='/bin/bash')
+                diff_out, error = process.communicate()
+
+                if diff_out.decode('ascii') != "":
+                    test = "False : {}".format(diff_out)
+                    false_cnt += 1
+                elif diff_out.decode('ascii') == "":
+                    test = True
+                    true_cnt += 1
+                else:
+                    print(error)
+
+                out = "Test result: {}\n".format(str(test))
+                f.write(out)
+                print(out)
+
+            elif file_usage == "not_empty":
+
+                test = os.path.getsize(observed_path) > 0
+
+                if test:
+                    true_cnt += 1
+                else:
+                    false_cnt += 1
+
+                out = "Test result: {}\n".format(str(test))
+                print(out)
+                f.write(out)
+
+            else:
+
+                sys.exit("\n{} is not valid\n".format(file_usage))
+
+            continue
+
+    true_perc = (float(true_cnt) / float(max_cnt) * 100)
+    if false_cnt != 0:
+        false_perc = 100 - (float(true_cnt) / float(max_cnt) * 100)
+    else:
+        false_perc = 0
+
+    out = """
+
+=========================================
+-----------------------------------------
+
+Testing the 01_clean_qc step of metagWGS:
+
+Total:      {}
+Passed:     {} ({}%)
+Missed:     {} ({}%)
+
+-----------------------------------------
+=========================================
+""".format(max_cnt, true_cnt, true_perc, false_cnt, false_perc)
+
+    f.write(out)
+    print(out)
+
+    f.close()
+
+# __main__
+def main():
+
+    global args
+    args = parse_arguments()
+    
+    if args.step not in steps_list:
+
+        sys.exit("-step doesn't exist, please chose from: {}".format(steps_list))
+
+    if args.script:
+
+        launch_nextflow(args.script)
+
+    if args.step == "01_clean_qc":
+
+        check_01_clean_qc(_01_1_cleaned_reads + _01_2_qc + _01_3_taxonomic_affiliation_reads)
+
+    else:
+
+        print("Step {}, nothing to do yet".format(args.step))
+
+if __name__ == "__main__":
+
+    main()
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