diff --git a/compose.yaml b/compose.yaml index 073b4ef..cab3dcd 100644 --- a/compose.yaml +++ b/compose.yaml @@ -3,7 +3,7 @@ services: run: build: . volumes: - - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/MiSEQ/:/PseudonymizedRuns + - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/PseudonymizedRunes:/PseudonymizedRuns - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/OrganisedRuns/:/OrganisedRuns - /home/houfek/Work/MMCI/sequencing_pipeline/data-catalogue-playground/muni-sc/Patients/:/Patients command: bash -c "python main.py diff --git a/main.py b/main.py index 08de3d1..bc737fe 100644 --- a/main.py +++ b/main.py @@ -1,41 +1,5 @@ import argparse -import os -import shutil -import logging -from datetime import datetime -from organiser.organise_run import RunOrganiser -from organiser.helpers.file_helpers import create_dictionary_if_not_exist - - -def _create_important_folders_if_not_exist(organisation_folder): - create_dictionary_if_not_exist(os.path.join(organisation_folder, "logs")) - create_dictionary_if_not_exist(os.path.join(organisation_folder, "backups")) - create_dictionary_if_not_exist(os.path.join(organisation_folder, "errors")) - - -def run(path_to_runs_for_processing, path_to_organisation_folder, path_to_patient_organisation_folder): - _create_important_folders_if_not_exist(path_to_organisation_folder) - logging.basicConfig(filename=os.path.join(path_to_organisation_folder, "logs", - datetime.now().strftime('%d_%m_%Y-%H_%M.log')), - encoding='utf-8', - level=logging.INFO) - - for file in os.listdir(path_to_runs_for_processing): - logging.info(f"Organising: {file}") - try: - RunOrganiser(path_to_runs_for_processing, file, - path_to_organisation_folder, path_to_patient_organisation_folder)() - except FileNotFoundError as e: - logging.error(f"Run {file} is missing some data\nError:\n{e}") - shutil.move(os.path.join(path_to_runs_for_processing, file), - os.path.join(path_to_organisation_folder, "errors", file)) - continue - - shutil.move(os.path.join(path_to_runs_for_processing, file), - os.path.join(path_to_organisation_folder, "backups", file)) - logging.info("File moved into backups") - - logging.info("Done!") +from organiser.process.processor import Processor if __name__ == "__main__": @@ -48,4 +12,4 @@ def run(path_to_runs_for_processing, path_to_organisation_folder, path_to_patien parser.add_argument("-p", "--patients", type=str, required=True, help="Path to a patient folder") args = parser.parse_args() - run(args.runs, args.output, args.patients) + Processor(args.runs, args.output, args.patients).process_runs() diff --git a/tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/CompletedJobInfo.xml b/organiser/process/__init__.py similarity index 100% rename from tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/CompletedJobInfo.xml rename to organiser/process/__init__.py diff --git a/organiser/process/processor.py b/organiser/process/processor.py new file mode 100644 index 0000000..8b8eeaa --- /dev/null +++ b/organiser/process/processor.py @@ -0,0 +1,64 @@ +import os +import shutil +import logging +import sys +from datetime import datetime +from organiser.run_organisers.old_miseq_organise_run import OldMiseqRunOrganiser +from organiser.run_organisers.new_miseq_organise_run import NewMiseqOrganiseRun +from organiser.run_organisers.organise_run import OrganiseRun +from organiser.helpers.file_helpers import create_dictionary_if_not_exist + + +class Processor: + def __init__(self, pseudnymized_runs_folder, folder_for_organised_files, patient_folder): + self.psedunymized_runs_folder = pseudnymized_runs_folder + self.organised_files_folder = folder_for_organised_files + self.patient_folder = patient_folder + + def process_runs(self): + self._create_important_folders_if_not_exist() + logging.basicConfig(filename=os.path.join(self.organised_files_folder, "logs", + datetime.now().strftime('%d_%m_%Y-%H_%M.log')), + encoding='utf-8', + level=logging.INFO) + logging.getLogger().addHandler(logging.StreamHandler(sys.stdout)) + + for run in os.listdir(self.psedunymized_runs_folder): + if run in ["backups", "logs", "errors"]: + continue + logging.info(f"Organising: {run}") + organiser = self._get_correct_organiser(run) + self._try_organise_run(run, organiser) + + logging.info("Done!") + + def _try_organise_run(self, run, organiser) -> bool: + try: + organiser.organise_run() + except FileNotFoundError as e: + logging.error(f"Run {run} is missing some data\nError:\n{e}") + shutil.move(os.path.join(self.psedunymized_runs_folder, run), + os.path.join(self.organised_files_folder, "errors", run)) + return False + + shutil.move(os.path.join(self.psedunymized_runs_folder, run), + os.path.join(self.organised_files_folder, "backups", run)) + logging.info(f"Run {run} moved into backups") + return True + + def _create_important_folders_if_not_exist(self): + create_dictionary_if_not_exist(os.path.join(self.organised_files_folder, "logs")) + create_dictionary_if_not_exist(os.path.join(self.organised_files_folder, "backups")) + create_dictionary_if_not_exist(os.path.join(self.organised_files_folder, "errors")) + + def _get_correct_organiser(self, run_path) -> OrganiseRun: + full_run_path = os.path.join(self.psedunymized_runs_folder, run_path) + + if "Alignment_1" in os.listdir(full_run_path) or "SoftwareVersionsFile" in os.listdir(full_run_path): + logging.info(f"{run_path} processed as New Miseq") + return NewMiseqOrganiseRun(self.psedunymized_runs_folder, run_path, + self.organised_files_folder, self.patient_folder) + else: + logging.info(f"{run_path} processed as Old Miseq") + return OldMiseqRunOrganiser(self.psedunymized_runs_folder, run_path, + self.organised_files_folder, self.patient_folder) diff --git a/tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/Samples/mmci_predictive_00000000-0000-0000-0000-000000000001/Analysis/Reports/mmci_predictive_00000000-0000-0000-0000-000000000001_Coverage_Curve_Report1.txt b/organiser/run_organisers/__init__.py similarity index 100% rename from tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/Samples/mmci_predictive_00000000-0000-0000-0000-000000000001/Analysis/Reports/mmci_predictive_00000000-0000-0000-0000-000000000001_Coverage_Curve_Report1.txt rename to organiser/run_organisers/__init__.py diff --git a/organiser/run_organisers/new_miseq_organise_run.py b/organiser/run_organisers/new_miseq_organise_run.py new file mode 100644 index 0000000..8f502d0 --- /dev/null +++ b/organiser/run_organisers/new_miseq_organise_run.py @@ -0,0 +1,61 @@ +import os +from pathlib import Path + +from organiser.helpers.file_helpers import copy_folder_if_exists, copy_if_exists +from .old_miseq_organise_run import OldMiseqRunOrganiser + + +class NewMiseqOrganiseRun(OldMiseqRunOrganiser): + + def organise_run(self): + y = self._get_file_year() + machine = "MiSEQ" + folder_for_run_path = os.path.join(self.organised_runs, y, machine) + Path(folder_for_run_path).mkdir(parents=True, exist_ok=True) + self._create_sample_dirs(folder_for_run_path) + self._create_general_file(folder_for_run_path) + self._create_patient_files_if_clinical_data_exist() + return os.path.join(folder_for_run_path, self.file) + + def _collect_data_for_pseudo_number(self, new_folder, pseudo_number): + fastq_folder = os.path.join(self.pseudo_run, self.file, "Alignment_1", "Fastq") + new_fastq_folder = os.path.join(new_folder, "FASTQ") + Path(new_fastq_folder).mkdir(parents=True, exist_ok=True) + + for file in os.listdir(fastq_folder): + if pseudo_number in file: + copy_if_exists(os.path.join(fastq_folder, file), + os.path.join(new_fastq_folder, file)) + + self._collect_analysis(new_folder, pseudo_number) + + def _create_general_file(self, new_file_path): + general_file_path = os.path.join(self.pseudo_run, self.file) + new_general_file_path = os.path.join(new_file_path, self.file) + Path(new_general_file_path).mkdir(parents=True, exist_ok=True) + + self._copy_important_files(general_file_path, new_general_file_path) + self._copy_important_folders(general_file_path, new_general_file_path) + + def _copy_important_files(self, old_path, new_path): + files_to_move = [ + os.path.join("Alignment_1", "AnalysisLog.txt"), + os.path.join("Alignment_1", "CompletedJobInfo.xml"), + "RunParameters.xml", + "RunInfo.xml", + "SampleSheet.csv", + "GenerateFASTQRunStatistics.xml" + ] + for file in files_to_move: + base = os.path.basename(file) + old_file_path = os.path.join(old_path, file) + new_file_path = os.path.join(new_path, os.path.basename(file)) + copy_if_exists(old_file_path, new_file_path) + + def _copy_important_folders(self, old_path, new_path): + folder_paths = [("Alignment_1", "Alignment"), + ("catalog_info_per_pred_number", "catalog_info_per_pred_number")] + for old, new in folder_paths: + old_folder_path = os.path.join(old_path, old) + new_folder_path = os.path.join(new_path, new) + copy_folder_if_exists(old_folder_path, new_folder_path) diff --git a/organiser/organise_run.py b/organiser/run_organisers/old_miseq_organise_run.py similarity index 53% rename from organiser/organise_run.py rename to organiser/run_organisers/old_miseq_organise_run.py index ccf720c..8abb1d8 100644 --- a/organiser/organise_run.py +++ b/organiser/run_organisers/old_miseq_organise_run.py @@ -5,10 +5,11 @@ import json import logging +from .organise_run import OrganiseRun from organiser.helpers.file_helpers import copy_folder_if_exists, copy_if_exists -class RunOrganiser: +class OldMiseqRunOrganiser(OrganiseRun): def __init__(self, path_to_pseudonymized_runs_folder, name_of_single_run, path_to_oragnised_storage, path_to_patients): @@ -17,82 +18,56 @@ def __init__(self, path_to_pseudonymized_runs_folder, name_of_single_run, self.organised_runs = path_to_oragnised_storage self.organised_patients = path_to_patients - def __call__(self): - return self.organise_run() - def organise_run(self): - y, machine, run_number = self._split_file_to_parts(self.file) - run_path = os.path.join(self.organised_runs, y, machine, run_number) - Path(run_path).mkdir(parents=True, exist_ok=True) - self._create_sample_dirs(run_path, self.file) - self._create_general_file(run_path, self.file) - self._create_patient_files_if_clinical_data_exist(self.file) - return os.path.join(y, machine, run_number, self.file) - - def _split_file_to_parts(self, filename): - splitted_filename = filename.split("_") + y = self._get_file_year() + machine = "MiSEQ" + folder_for_run_path = os.path.join(self.organised_runs, y, machine) + Path(folder_for_run_path).mkdir(parents=True, exist_ok=True) + self._create_sample_dirs(folder_for_run_path) + self._create_general_file(folder_for_run_path) + self._create_patient_files_if_clinical_data_exist() + return os.path.join(folder_for_run_path, self.file) + + def _get_file_year(self): + splitted_filename = self.file.split("_") year = splitted_filename[0][:2] - if splitted_filename[1][0] == "M": - machine = "MiSEQ" - run_number = splitted_filename[1][1:] - else: - machine = "NextSEQ" - run_number = splitted_filename[1][2:] - - return f"20{year}", machine, run_number - - def _create_sample_dirs(self, run_path, filename): - sample_sheet_path = os.path.join(self.pseudo_run, filename, "SampleSheet.csv") + return f"20{year}" + + def _create_sample_dirs(self, run_samples_path): + sample_sheet_path = os.path.join(self.pseudo_run, self.file, "SampleSheet.csv") pseudo_numbers = self._get_pseudo_numbers(sample_sheet_path) - run_path = os.path.join(run_path, filename, "Samples") - Path(run_path).mkdir(parents=True, exist_ok=True) + run_samples_path = os.path.join(run_samples_path, self.file, "Samples") + Path(run_samples_path).mkdir(parents=True, exist_ok=True) for pseudo_number in pseudo_numbers: - new_pseudo_folder = os.path.join(run_path, pseudo_number) + new_pseudo_folder = os.path.join(run_samples_path, pseudo_number) Path(new_pseudo_folder).mkdir(parents=True, exist_ok=True) - self._collect_data_for_pseudo_number(filename, new_pseudo_folder, pseudo_number) + self._collect_data_for_pseudo_number(new_pseudo_folder, pseudo_number) - def _create_general_file(self, new_file_path, file): - general_file_path = os.path.join(self.pseudo_run, file) - new_general_file_path = os.path.join(new_file_path, file) + def _create_general_file(self, new_file_path): + general_file_path = os.path.join(self.pseudo_run, self.file) + new_general_file_path = os.path.join(new_file_path, self.file) Path(new_general_file_path).mkdir(parents=True, exist_ok=True) - run_parameters = os.path.join(general_file_path, "runParameters.xml") - new_run_parameters = os.path.join(new_general_file_path, "runParameters.xml") - copy_if_exists(run_parameters, new_run_parameters) - - run_info = os.path.join(general_file_path, "RunInfo.xml") - new_run_info = os.path.join(new_general_file_path, "RunInfo.xml") - copy_if_exists(run_info, new_run_info) - - completed_job = os.path.join(general_file_path, "CompletedJobInfo.xml") - new_completed_job = os.path.join(new_general_file_path, "CompletedJobInfo.xml") - copy_if_exists(completed_job, new_completed_job) + self._copy_important_files(general_file_path, new_general_file_path) + self._copy_important_folders(general_file_path, new_general_file_path) - generate_statistics = os.path.join(general_file_path, "GenerateFASTQRunStatistics.xml") - new_generate_statistics = os.path.join(new_general_file_path, "GenerateFASTQRunStatistics.xml") - copy_if_exists(generate_statistics, new_generate_statistics) + def _copy_important_files(self, old_path, new_path): + files_to_move = ["runParameters.xml", "RunInfo.xml", "CompletedJobInfo.xml", + "GenerateFASTQRunStatistics.xml", "AnalysisLog.txt", "SampleSheet.csv"] - analysis_log = os.path.join(general_file_path, "AnalysisLog.txt") - new_analysis_log = os.path.join(new_general_file_path, "AnalysisLog.txt") - copy_if_exists(analysis_log, new_analysis_log) + for file in files_to_move: + run_parameters = os.path.join(old_path, file) + new_run_parameters = os.path.join(new_path, file) + copy_if_exists(run_parameters, new_run_parameters) - sample_sheet = os.path.join(general_file_path, "SampleSheet.csv") - new_sample_sheet = os.path.join(new_general_file_path, "SampleSheet.csv") - copy_if_exists(sample_sheet, new_sample_sheet) - - data_intensities_basecalls_alignments = os.path.join(general_file_path, "Data", - "Intensities", "BaseCalls", "Alignment") - new_data_intenstisities_basecalls_alignment = os.path.join(new_general_file_path, "Data", - "Intensities", "BaseCalls") - Path(new_data_intenstisities_basecalls_alignment).mkdir(parents=True, exist_ok=True) - copy_folder_if_exists( - data_intensities_basecalls_alignments, - os.path.join(new_data_intenstisities_basecalls_alignment, "Alignment")) - - catalog_info_per_pac = os.path.join(general_file_path, "catalog_info_per_pred_number") - new_catalog_info_per_pac = os.path.join(new_general_file_path, "catalog_info_per_pred_number") - copy_folder_if_exists(catalog_info_per_pac, new_catalog_info_per_pac) + def _copy_important_folders(self, old_path, new_path): + folder_paths = [os.path.join("Data", "Intensities", "BaseCalls", "Alignment"), + "catalog_info_per_pred_number"] + for folder in folder_paths: + old_folder_path = os.path.join(old_path, folder) + new_folder_path = os.path.join(new_path, os.path.basename(folder)) + copy_folder_if_exists(old_folder_path, new_folder_path) def _get_pseudo_numbers(self, sample_sheet_path): df = pd.read_csv(sample_sheet_path, delimiter=",", @@ -104,17 +79,21 @@ def _get_pseudo_numbers(self, sample_sheet_path): return pseudo_numbers - def _collect_data_for_pseudo_number(self, filename, new_folder, pseudo_number): - basecalls = os.path.join(self.pseudo_run, filename, "Data", "Intensities", "BaseCalls") + def _collect_data_for_pseudo_number(self, new_folder, pseudo_number): + basecalls = os.path.join(self.pseudo_run, self.file, "Data", "Intensities", "BaseCalls") + new_fastq_folder = os.path.join(new_folder, "FASTQ") Path(new_fastq_folder).mkdir(parents=True, exist_ok=True) for file in os.listdir(basecalls): if pseudo_number in file: - copy_if_exists(os.path.join(basecalls, file), os.path.join(new_fastq_folder, file)) + copy_if_exists(os.path.join(basecalls, file), + os.path.join(new_fastq_folder, file)) + + self._collect_analysis(new_folder, pseudo_number) - # analysis - analysis = os.path.join(self.pseudo_run, filename, "Analysis") + def _collect_analysis(self, new_folder, pseudo_number): + analysis = os.path.join(self.pseudo_run, self.file, "Analysis") if os.path.exists(analysis): new_analysis = os.path.join(new_folder, "Analysis") Path(new_analysis).mkdir(parents=True, exist_ok=True) @@ -165,8 +144,8 @@ def _get_convert(self, path, new_path): if file.endswith("RemoveDuplicates.log"): shutil.copy2(os.path.join(path, file), os.path.join(new_path, file)) - def _create_patient_files_if_clinical_data_exist(self, run_file): - clinical_info_path = os.path.join(self.pseudo_run, run_file, "catalog_info_per_pred_number") + def _create_patient_files_if_clinical_data_exist(self): + clinical_info_path = os.path.join(self.pseudo_run, self.file, "catalog_info_per_pred_number") if not os.path.exists(clinical_info_path): return diff --git a/organiser/run_organisers/organise_run.py b/organiser/run_organisers/organise_run.py new file mode 100644 index 0000000..306233c --- /dev/null +++ b/organiser/run_organisers/organise_run.py @@ -0,0 +1,8 @@ +from abc import ABC, abstractmethod + + +class OrganiseRun(ABC): + + @abstractmethod + def organise_run(self): + ... diff --git a/tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/Samples/mmci_predictive_00000000-0000-0000-0000-000000000002/Analysis/mmci_predictive_00000000-0000-0000-0000-000000000002_Parameters.txt b/tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/Samples/mmci_predictive_00000000-0000-0000-0000-000000000002/Analysis/mmci_predictive_00000000-0000-0000-0000-000000000002_Parameters.txt deleted file mode 100644 index e8325f2..0000000 --- a/tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/Samples/mmci_predictive_00000000-0000-0000-0000-000000000002/Analysis/mmci_predictive_00000000-0000-0000-0000-000000000002_Parameters.txt +++ /dev/null @@ -1,54 +0,0 @@ -SoftGenetics NextGENe V2.4.2.2 -leden/01/2015 - -[GENERAL] -User: -Instrument Type: Illumina -Application Type: SNP/Indel Discovery - -Steps: -Do Condensation: FALSE -Do Assembly: FALSE -Do Alignment: TRUE - -[Sequence Alignment] -Whole Gene Project: TRUE -Directory of Index:F:\Fake -Do WGA With Paired Index: FALSE -Reads:Allowable Mismatched Bases 1 -Allowable Ambiguous Alignments 50 -Seed: 21 Bases, Move Step: 5 Bases -Allowable Alignments 100 -Overall: Matching Base Percentage >= 90,0 -Detect Large Indels:TRUE -Sequence Range Checked: FALSE -Hide Unmatched Ends: TRUE -Except for Homozygous:TRUE -Mutation Filter Use Original:FALSE -Variation Mutation Percentage <= 3,00 -Variation SNP Allele <= 9 Counts -Variation Total Coverage <= 300 -Indels Mutation Percentage <= 3,00 -Indels SNP Allele <= 9 Counts -Indels Total Coverage <= 300 -HomoIndels Mutation Percentage <= 3,00 -HomoIndels SNP Allele <= 9 Counts -HomoIndels Total Coverage <= 300 -Perform in-read phasing:TRUE -Max gap between two variants 1 (0-3) -Phaseable reads percentage >= 50,00 -Max Phase alleles count:3 -Load Assembled Result Files: FALSE -Load Sage Data:FALSE -Load Paired Reads:TRUE - Min Pair End Gap:100 - Max Pair End Gap:1000 -Save Matched Reads:FALSE -Highlight Anchor Sequence:FALSE -Ambiguous Gain/Loss:TRUE -Detect Structure Variations:FALSE -Check Mismatch Base Number: TRUE 50 Bases -Check Mismatch Ratio: TRUE 0,300 Length - -[Reports] -AutoPostRptSaveAsPDF=0 \ No newline at end of file diff --git a/tests/test_organise_new_miseq_run.py b/tests/test_organise_new_miseq_run.py new file mode 100644 index 0000000..2db5f08 --- /dev/null +++ b/tests/test_organise_new_miseq_run.py @@ -0,0 +1,124 @@ +import pytest +import os +import shutil + +from organiser.run_organisers.new_miseq_organise_run import NewMiseqOrganiseRun + +FAKE_ALL_RUNS_FOR_TESTING = os.path.join(os.path.dirname(__file__), "FAKE_PSEUDONYMIZED_RUNS") +FAKE_RUN_FOR_COPY = os.path.join(os.path.dirname(__file__), "test_pseudonymized_runs", + "240101_M00000_0000_00000000-00000") + + +FAKE_RUN_FOR_TESTING = os.path.join(FAKE_ALL_RUNS_FOR_TESTING, "240101_M00000_0000_00000000-00000") +FAKE_DESTINATION_FILES = os.path.join(os.path.dirname(__file__), "test_destination") +FAKE_PATIENT_FILES = os.path.join(os.path.dirname(__file__), "test_patients") + + +EXPECTED_ORGANISED_FILE_PATH = os.path.join(FAKE_DESTINATION_FILES, + "2024", + "MiSEQ", + "240101_M00000_0000_00000000-00000") + + +def _copy_fake_run(): + shutil.copytree(FAKE_RUN_FOR_COPY, FAKE_RUN_FOR_TESTING) + os.mkdir(FAKE_DESTINATION_FILES) + os.mkdir(FAKE_PATIENT_FILES) + + +@pytest.fixture() +def remove_analysis_from_pseudonymized_file(): + shutil.rmtree(os.path.join(FAKE_RUN_FOR_TESTING, "Analysis")) + + +def _remove_coppied_fake_run(): + shutil.rmtree(FAKE_ALL_RUNS_FOR_TESTING) + shutil.rmtree(FAKE_PATIENT_FILES) + shutil.rmtree(FAKE_DESTINATION_FILES) + + +@pytest.fixture(autouse=True) +def setup_and_teardown_organise_files(request): + _copy_fake_run() + request.addfinalizer(_remove_coppied_fake_run) + + +def get_organiser(): + return NewMiseqOrganiseRun(FAKE_ALL_RUNS_FOR_TESTING, "240101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + + +def test_folder_structure_correct(): + organiser = get_organiser() + organiser.organise_run() + + assert os.path.exists(EXPECTED_ORGANISED_FILE_PATH) + + +def test_alignment_correct(): + organiser = get_organiser() + organiser.organise_run() + + assert os.path.exists(os.path.join(EXPECTED_ORGANISED_FILE_PATH, "Alignment")) + + +def test_catalog_info_per_pred_number(): + organiser = get_organiser() + organiser.organise_run() + + assert os.path.exists(os.path.join(EXPECTED_ORGANISED_FILE_PATH, "catalog_info_per_pred_number")) + + +def test_catalog_info_missing_no_error(remove_catalog_info_per_pred_number): + organiser = get_organiser() + organiser.organise_run() + + assert not os.path.exists(os.path.join(EXPECTED_ORGANISED_FILE_PATH, "catalog_info_per_pred_number")) + + +def test_important_files_coppied(): + important_files = ["AnalysisLog.txt", "CompletedJobInfo.xml", "RunParameters.xml", + "RunInfo.xml", "SampleSheet.csv", "GenerateFASTQRunStatistics.xml"] + organiser = get_organiser() + organiser.organise_run() + for file in important_files: + assert os.path.exists(os.path.join(EXPECTED_ORGANISED_FILE_PATH, file)) + + +def test_fastq_files_coppied(): + organiser = get_organiser() + organiser.organise_run() + for i in range(1, 20): + assert os.path.exists(os.path.join(EXPECTED_ORGANISED_FILE_PATH, + "Samples", + f"mmci_predictive_00000000-0000-0000-0000-0000000000{str(i).zfill(2)}", + "FASTQ")) + + +def test_analysis_files(): + organiser = get_organiser() + organiser.organise_run() + + for i in range(1, 20): + predictive_path = f"mmci_predictive_00000000-0000-0000-0000-0000000000{str(i).zfill(2)}" + expected_path_to_analysis = os.path.join(EXPECTED_ORGANISED_FILE_PATH, "Samples", predictive_path, "Analysis") + assert os.path.exists(expected_path_to_analysis) + assert os.path.exists(os.path.join(expected_path_to_analysis, "Reports")) + + assert os.path.exists(os.path.join(expected_path_to_analysis, f"{predictive_path}.bam")) + assert os.path.exists(os.path.join(expected_path_to_analysis, f"{predictive_path}.bam.bai")) + + assert os.path.exists(os.path.join(expected_path_to_analysis, f"{predictive_path}_Parameters.txt")) + assert os.path.exists(os.path.join(expected_path_to_analysis, f"{predictive_path}_StatInfo.txt")) + + assert os.path.exists(os.path.join(expected_path_to_analysis, f"{predictive_path}_S6_L001_R1_001_convert.log")) + assert os.path.exists(os.path.join(expected_path_to_analysis, + f"{predictive_path}_S6_L001_R1_001_converted.fasta")) + assert os.path.exists(os.path.join(expected_path_to_analysis, f"{predictive_path}_S6_L001_R2_001_convert.log")) + assert os.path.exists(os.path.join(expected_path_to_analysis, + f"{predictive_path}_S6_L001_R2_001_converted.fasta")) + + +@pytest.fixture +def remove_catalog_info_per_pred_number(): + shutil.rmtree(os.path.join(FAKE_RUN_FOR_TESTING, "catalog_info_per_pred_number")) diff --git a/tests/test_organise_run.py b/tests/test_organise_old_miseq_run.py similarity index 67% rename from tests/test_organise_run.py rename to tests/test_organise_old_miseq_run.py index e685f21..dba96a8 100644 --- a/tests/test_organise_run.py +++ b/tests/test_organise_old_miseq_run.py @@ -2,14 +2,14 @@ import os import shutil -from organiser.organise_run import RunOrganiser +from organiser.run_organisers.old_miseq_organise_run import OldMiseqRunOrganiser FAKE_ALL_RUNS_FOR_TESTING = os.path.join(os.path.dirname(__file__), "FAKE_PSEUDONYMIZED_RUNS") FAKE_RUN_FOR_COPY = os.path.join(os.path.dirname(__file__), "test_pseudonymized_runs", - "2020_M00000_0000_00000000-00000") + "200101_M00000_0000_00000000-00000") -FAKE_RUN_FOR_TESTING = os.path.join(FAKE_ALL_RUNS_FOR_TESTING, "2020_M00000_0000_00000000-00000") +FAKE_RUN_FOR_TESTING = os.path.join(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000") FAKE_DESTINATION_FILES = os.path.join(os.path.dirname(__file__), "test_destination") FAKE_PATIENT_FILES = os.path.join(os.path.dirname(__file__), "test_patients") @@ -38,22 +38,22 @@ def setup_and_teardown_organise_files(request): def test_folder_structure_correct(): - organiser = RunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "2020_M00000_0000_00000000-00000", - FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + organiser = OldMiseqRunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) organiser.organise_run() - assert os.path.exists(os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", "00000", - "2020_M00000_0000_00000000-00000")) + assert os.path.exists(os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", + "200101_M00000_0000_00000000-00000")) @pytest.mark.parametrize("id_part", ["1", "5", "9"]) def test_correct_files_fastq(id_part): - organiser = RunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "2020_M00000_0000_00000000-00000", - FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + organiser = OldMiseqRunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) organiser.organise_run() - expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", "00000", - "2020_M00000_0000_00000000-00000") + expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", + "200101_M00000_0000_00000000-00000") predictive_number = f"mmci_predictive_00000000-0000-0000-0000-00000000000{id_part}" @@ -65,12 +65,12 @@ def test_correct_files_fastq(id_part): @pytest.mark.parametrize("id_part", ["1", "5", "9"]) def test_correct_analysis_files(id_part): - organiser = RunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "2020_M00000_0000_00000000-00000", - FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + organiser = OldMiseqRunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) organiser.organise_run() - expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", "00000", - "2020_M00000_0000_00000000-00000") + expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", + "200101_M00000_0000_00000000-00000") predictive_number = f"mmci_predictive_00000000-0000-0000-0000-00000000000{id_part}" @@ -88,12 +88,12 @@ def test_correct_analysis_files(id_part): @pytest.mark.parametrize("id_part", ["1", "5", "9"]) def test_correct_report_files(id_part): - organiser = RunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "2020_M00000_0000_00000000-00000", - FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + organiser = OldMiseqRunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) organiser.organise_run() - expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", "00000", - "2020_M00000_0000_00000000-00000") + expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", + "200101_M00000_0000_00000000-00000") predictive_number = f"mmci_predictive_00000000-0000-0000-0000-00000000000{id_part}" @@ -111,12 +111,12 @@ def test_correct_report_files(id_part): @pytest.mark.parametrize("id_part", ["1", "5", "9"]) def test_organise_without_analysis(id_part, remove_analysis_from_pseudonymized_file): - organiser = RunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "2020_M00000_0000_00000000-00000", - FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + organiser = OldMiseqRunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) organiser.organise_run() - expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", "00000", - "2020_M00000_0000_00000000-00000") + expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", + "200101_M00000_0000_00000000-00000") predictive_number = f"mmci_predictive_00000000-0000-0000-0000-00000000000{id_part}" @@ -126,14 +126,25 @@ def test_organise_without_analysis(id_part, remove_analysis_from_pseudonymized_f def test_important_run_metadata_files(): - organiser = RunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "2020_M00000_0000_00000000-00000", - FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + organiser = OldMiseqRunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) organiser.organise_run() - expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", "00000", - "2020_M00000_0000_00000000-00000") + expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", + "200101_M00000_0000_00000000-00000") assert os.path.exists(os.path.join(expected_run_folder, "runParameters.xml")) assert os.path.exists(os.path.join(expected_run_folder, "GenerateFASTQRunStatistics.xml")) assert os.path.exists(os.path.join(expected_run_folder, "RunInfo.xml")) assert os.path.exists(os.path.join(expected_run_folder, "AnalysisLog.txt")) + + +def test_alignment_folder(): + organiser = OldMiseqRunOrganiser(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000", + FAKE_DESTINATION_FILES, FAKE_PATIENT_FILES) + organiser.organise_run() + + expected_run_folder = os.path.join(FAKE_DESTINATION_FILES, "2020", "MiSEQ", + "200101_M00000_0000_00000000-00000") + + assert os.path.exists(os.path.join(expected_run_folder, "Alignment")) diff --git a/tests/test_processor.py b/tests/test_processor.py new file mode 100644 index 0000000..233c79c --- /dev/null +++ b/tests/test_processor.py @@ -0,0 +1,81 @@ +import pytest +import os +import shutil +from organiser.process.processor import Processor + +FAKE_ALL_RUNS_FOR_TESTING = os.path.join(os.path.dirname(__file__), "FAKE_PSEUDONYMIZED_RUNS") +FAKE_ALL_RUNS_FOR_COPY = os.path.join(os.path.dirname(__file__), "test_pseudonymized_runs") + +FAKE_DESTINATION_FILES = os.path.join(os.path.dirname(__file__), "test_destination") +FAKE_PATIENT_FILES = os.path.join(os.path.dirname(__file__), "test_patients") + +FAKE_OLD_MISEQ_PATH = os.path.join(FAKE_ALL_RUNS_FOR_COPY, "200101_M00000_0000_00000000-00000") +FAKE_NEW_MISEQ_PATH = os.path.join(FAKE_ALL_RUNS_FOR_COPY, "240101_M00000_0000_00000000-00000") + +FAKE_OLD_MISEQ_FOR_TESTING = os.path.join(FAKE_ALL_RUNS_FOR_TESTING, "200101_M00000_0000_00000000-00000") +FAKE_NEW_MISEQ_FOR_TESTING = os.path.join(FAKE_ALL_RUNS_FOR_TESTING, "240101_M00000_0000_00000000-00000") + + +def _copy_fake_folders(): + os.mkdir(FAKE_PATIENT_FILES) + os.mkdir(FAKE_DESTINATION_FILES) + + +def _remove_coppied_fake_run(): + shutil.rmtree(FAKE_ALL_RUNS_FOR_TESTING) + shutil.rmtree(FAKE_PATIENT_FILES) + shutil.rmtree(FAKE_DESTINATION_FILES) + + +@pytest.fixture(autouse=True) +def setup_and_teardown_test_files(request): + _copy_fake_folders() + request.addfinalizer(_remove_coppied_fake_run) + + +@pytest.fixture +def setup_and_teardown_old_miseq(): + shutil.copytree(FAKE_OLD_MISEQ_PATH, FAKE_OLD_MISEQ_FOR_TESTING) + + +@pytest.fixture +def setup_and_teardown_new_miseq(): + shutil.copytree(FAKE_NEW_MISEQ_PATH, FAKE_NEW_MISEQ_FOR_TESTING) + + +@pytest.fixture +def mocked_old_miseq_organise_run(mocker): + return mocker.patch("organiser.run_organisers.old_miseq_organise_run.OldMiseqRunOrganiser.organise_run") + + +@pytest.fixture +def mocked_new_miseq_organise_run(mocker): + return mocker.patch("organiser.run_organisers.new_miseq_organise_run.NewMiseqOrganiseRun.organise_run") + + +def test_select_old_miseq(setup_and_teardown_old_miseq, mocked_old_miseq_organise_run, mocked_new_miseq_organise_run): + processor = Processor(FAKE_ALL_RUNS_FOR_TESTING, + FAKE_DESTINATION_FILES, + FAKE_PATIENT_FILES) + processor.process_runs() + mocked_old_miseq_organise_run.assert_called_once() + mocked_new_miseq_organise_run.assert_not_called() + + +def test_select_new_miseq(setup_and_teardown_new_miseq, mocked_new_miseq_organise_run, mocked_old_miseq_organise_run): + processor = Processor(FAKE_ALL_RUNS_FOR_TESTING, + FAKE_DESTINATION_FILES, + FAKE_PATIENT_FILES) + processor.process_runs() + mocked_new_miseq_organise_run.assert_called_once() + mocked_old_miseq_organise_run.assert_not_called() + + +def test_new_and_old_miseq_called(setup_and_teardown_new_miseq, setup_and_teardown_old_miseq, + mocked_new_miseq_organise_run, mocked_old_miseq_organise_run): + processor = Processor(FAKE_ALL_RUNS_FOR_TESTING, + FAKE_DESTINATION_FILES, + FAKE_PATIENT_FILES) + processor.process_runs() + mocked_new_miseq_organise_run.assert_called_once() + mocked_old_miseq_organise_run.assert_called_once() diff --git a/tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/Samples/mmci_predictive_00000000-0000-0000-0000-000000000001/Analysis/mmci_predictive_00000000-0000-0000-0000-000000000001.bam b/tests/test_pseudonymized_runs/200101_M00000_0000_00000000-00000/Analysis/BAM/mmci_predictive_00000000-0000-0000-0000-000000000001.bam similarity index 100% rename from tests/test_destination_for_copy/2020/MiSEQ/00000/2020_M00000_0000_00000000-00000/Samples/mmci_predictive_00000000-0000-0000-0000-000000000001/Analysis/mmci_predictive_00000000-0000-0000-0000-000000000001.bam rename to 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