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00:00:00 2001 From: Vedran Kasalica Date: Mon, 8 Jul 2024 13:41:22 +0200 Subject: [PATCH 2/6] Add the initial GH Action --- .github/workflows/build.yml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 .github/workflows/build.yml diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..aa7bcc7 --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,37 @@ +name: Build and test + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + build-and-test: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.9'] + outputs: + version: ${{ steps.get_version.outputs.version }} + + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + python -m pip install poetry + poetry install + # - name: Test with pytest + # run: | + # poetry run pytest + - name: Build the package + run: | + poetry build \ No newline at end of file From 51a5f3b8724d4a97133162dd51a1fe95dd999e49 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Mon, 8 Jul 2024 14:13:40 +0200 Subject: [PATCH 3/6] Try docker GH Action --- .github/workflows/build.yml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index aa7bcc7..32a67d3 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -12,14 +12,17 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] outputs: version: ${{ steps.get_version.outputs.version }} steps: - - uses: actions/checkout@v4 - with: - fetch-depth: 0 + - name: Checkout repository + uses: actions/checkout@v4 + + - name: Set up Docker + uses: docker/setup-buildx-action@v2 + - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 with: From 715752db28a7a64ef7a8204e0184c5ba8573c86c Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Mon, 8 Jul 2024 14:57:58 +0200 Subject: [PATCH 4/6] Improve UI and setup tests --- .github/workflows/build.yml | 6 +-- .gitignore | 3 ++ src/workflomics_benchmarker/cwltool_runner.py | 30 +++++++++++---- .../cwltool_wrapper.py | 37 ++++++++++++++++--- src/workflomics_benchmarker/workflomics.py | 2 + 5 files changed, 61 insertions(+), 17 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 32a67d3..2abf971 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -32,9 +32,9 @@ jobs: run: | python -m pip install poetry poetry install - # - name: Test with pytest - # run: | - # poetry run pytest + - name: Test with pytest + run: | + poetry run pytest - name: Build the package run: | poetry build \ No newline at end of file diff --git a/.gitignore b/.gitignore index 0466522..aaa9493 100644 --- a/.gitignore +++ b/.gitignore @@ -147,3 +147,6 @@ dmypy.json tests/data/benchmarks.json tests/data/workflow.cwl_output/* src/workflomics_benchmarker/to_implement.py +tests/data/workflow_output/* +tests/data/workflow_fail_output/* +tests/data/workflow_fail2_output/* diff --git a/src/workflomics_benchmarker/cwltool_runner.py b/src/workflomics_benchmarker/cwltool_runner.py index 9066a9d..d9a1ee1 100644 --- a/src/workflomics_benchmarker/cwltool_runner.py +++ b/src/workflomics_benchmarker/cwltool_runner.py @@ -5,12 +5,14 @@ from workflomics_benchmarker.cwltool_wrapper import CWLToolWrapper from workflomics_benchmarker.loggingwrapper import LoggingWrapper + class CWLToolRunner(CWLToolWrapper): """ Class to manage and run CWL (Common Workflow Language) workflows. """ - success_workflows : list = [] - failed_workflows : list = [] + + success_workflows: list = [] + failed_workflows: list = [] def __init__(self, args): """ @@ -37,15 +39,21 @@ def _construct_command(self, workflow_path): list A list of command segments to execute the workflow. """ - base_command = ['cwltool --on-error continue'] + base_command = ["cwltool"] if self.container == "singularity": - base_command.append('--singularity') + base_command.append("--singularity") workflow_name = Path(workflow_path).stem output_directory = os.path.join(self.outdir, f"{workflow_name}_output") Path(output_directory).mkdir(exist_ok=True) - return base_command + ['--outdir', output_directory, workflow_path, self.input_yaml_path], output_directory + base_command.extend(["--on-error", "continue"]) + + return ( + base_command + + ["--outdir", output_directory, workflow_path, self.input_yaml_path], + output_directory, + ) def _execute_command(self, command, workflow_name): """ @@ -63,11 +71,15 @@ def _execute_command(self, command, workflow_name): bool True if the workflow executed successfully, False otherwise. """ - result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True) + result = subprocess.run( + command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, text=True + ) print(result.stdout) if result.returncode == 0: - LoggingWrapper.info(f"Workflow {workflow_name} finished successfully.", color="green") + LoggingWrapper.info( + f"Workflow {workflow_name} finished successfully.", color="green" + ) return True else: LoggingWrapper.error(f"Workflow {workflow_name} failed.", color="red") @@ -97,4 +109,6 @@ def run_workflows(self): for workflow_path in self.workflows: self.execute_workflow(workflow_path) total_workflows = len(self.success_workflows) + len(self.failed_workflows) - LoggingWrapper.info(f"Execution summary: {total_workflows} total, {len(self.success_workflows)} succeeded, {len(self.failed_workflows)} failed.") + LoggingWrapper.info( + f"Execution summary: {total_workflows} total, {len(self.success_workflows)} succeeded, {len(self.failed_workflows)} failed." + ) diff --git a/src/workflomics_benchmarker/cwltool_wrapper.py b/src/workflomics_benchmarker/cwltool_wrapper.py index c80345e..2bf87d4 100644 --- a/src/workflomics_benchmarker/cwltool_wrapper.py +++ b/src/workflomics_benchmarker/cwltool_wrapper.py @@ -33,7 +33,12 @@ def __init__(self, args): self.workflows = sorted([str(file) for file in Path(args.workflows).glob('*.cwl')], key=natural_keys) self.version = self.check_cwltool() - self.input = self.update_input_yaml(self.input_yaml_path) + if hasattr(args, 'interactive'): + interactive = True + else: + interactive = False + + self.input = self.update_input_yaml(self.input_yaml_path, interactive) def check_cwltool(self): @@ -47,24 +52,44 @@ def check_cwltool(self): print("cwltool is not installed.") return version - def update_input_yaml(self, input_yaml_path): - """Update the input yaml file with the paths to the input files""" + def update_input_yaml(self, input_yaml_path:str, interactive: bool) -> dict: + """ + Update the input yaml file with the paths to the input files. + If interactive is set to True, the user will be allowed to edit the paths to the input files. + + Parameters + ---------- + input_yaml_path : str + The path to the input yaml file. + + interactive : bool + If True, the user will be allowed to edit the paths to the input files. + + Returns + ------- + dict + A dictionary containing the input file names. + """ inputs = {} with open(input_yaml_path, 'r') as file: input_data = yaml.safe_load(file) for key, value in input_data.items(): if key.startswith('input'): - print(f"The path for {key} is {value['path']}. Do you want to change it? (y/n)") + if not interactive: + inputs[key] = {"filename": Path(value['path']).name} + continue + + print(f"The path for {key} is {value['path']}. Would you like to keep this path? ([Y]/n)") answer = input() - if answer == 'y': + if answer == 'n': new_path = input(f"Enter the path for {key}: ") value['path'] = new_path.strip() inputs[key] = {"filename": Path(value['path']).name} else: inputs[key] = {"filename": Path(value['path']).name} with open(input_yaml_path, 'w') as file: - documents = yaml.dump(input_data, file) + yaml.dump(input_data, file) return inputs diff --git a/src/workflomics_benchmarker/workflomics.py b/src/workflomics_benchmarker/workflomics.py index 493437d..75eff24 100644 --- a/src/workflomics_benchmarker/workflomics.py +++ b/src/workflomics_benchmarker/workflomics.py @@ -9,6 +9,7 @@ def add_benchmark_args(parser): """Add the arguments for the benchmark command.""" parser.add_argument('--singularity', action='store_true', help='Use singularity instead of docker.') + parser.add_argument('--interactive', action='store_true', help='Allow the user to interact with the library while running, e.g., to edit the paths to the input files before executing the workflows.') parser.add_argument('-o','--outdir', help='Path to the output directory to store the results (default: workflows directory).', default= None) parser.add_argument('-v', '--verbose', action='store_true', help='Print the output of the cwltool command.') parser.add_argument('-i','--input', help='Path to the input yaml file (default: input.yml in the workflows directory).', default= None) @@ -17,6 +18,7 @@ def add_benchmark_args(parser): def add_run_args(parser): """Add the arguments for the run command.""" parser.add_argument('--singularity', action='store_true', help='Use singularity instead of docker.') + parser.add_argument('--interactive', action='store_true', help='Allow the user to interact with the library while running, e.g., to edit the paths to the input files before executing the workflows.') parser.add_argument('-o','--outdir', help='Path to the output directory to store the results (default: workflows directory).', default= None) parser.add_argument('-v', '--verbose', action='store_true', help='Print the output of the cwltool command.') parser.add_argument('-i','--input', help='Path to the input yaml file (default: input.yml in the workflows directory).', default= None) From 4258b14c1628540d763e514012a0051e56aaaca5 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Mon, 8 Jul 2024 15:08:53 +0200 Subject: [PATCH 5/6] Fix readme --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index aad0376..2eeb9d9 100644 --- a/README.md +++ b/README.md @@ -91,7 +91,7 @@ python src/benchmarker/workflomics.py benchmark tests/data/ --singularity Run the following command to execute tests: ```bash -poetry run pytest -s +poetry run pytest ``` This command runs a workflow and benchmarks it, assuming Docker is operational. Results are stored in the `./tests/data` directory. From b77167899e802e2491e3b57d6ad934c22efcc9b7 Mon Sep 17 00:00:00 2001 From: Vedran Kasalica Date: Wed, 10 Jul 2024 15:20:03 +0200 Subject: [PATCH 6/6] Fix the interactive mode and bump the version --- .gitignore | 5 +---- pyproject.toml | 2 +- src/workflomics_benchmarker/cwltool_wrapper.py | 6 +++--- 3 files changed, 5 insertions(+), 8 deletions(-) diff --git a/.gitignore b/.gitignore index aaa9493..69144ed 100644 --- a/.gitignore +++ b/.gitignore @@ -145,8 +145,5 @@ dmypy.json .vscode/ tests/data/benchmarks.json -tests/data/workflow.cwl_output/* src/workflomics_benchmarker/to_implement.py -tests/data/workflow_output/* -tests/data/workflow_fail_output/* -tests/data/workflow_fail2_output/* +tests/data/workflow_*/* diff --git a/pyproject.toml b/pyproject.toml index e39e07b..c207743 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "workflomics-benchmarker" -version = "0.2.1" +version = "0.2.2" description = "Library used to execute workflows (in CWL) and benchmark them as part of the Workflomics ecosystem." authors = ["Vedran Kasalica ", "Nauman Ahmed ", diff --git a/src/workflomics_benchmarker/cwltool_wrapper.py b/src/workflomics_benchmarker/cwltool_wrapper.py index 2bf87d4..fb7a0c8 100644 --- a/src/workflomics_benchmarker/cwltool_wrapper.py +++ b/src/workflomics_benchmarker/cwltool_wrapper.py @@ -33,7 +33,7 @@ def __init__(self, args): self.workflows = sorted([str(file) for file in Path(args.workflows).glob('*.cwl')], key=natural_keys) self.version = self.check_cwltool() - if hasattr(args, 'interactive'): + if hasattr(args, 'interactive') and args.interactive: interactive = True else: interactive = False @@ -81,8 +81,8 @@ def update_input_yaml(self, input_yaml_path:str, interactive: bool) -> dict: continue print(f"The path for {key} is {value['path']}. Would you like to keep this path? ([Y]/n)") - answer = input() - if answer == 'n': + answer = input().lower() + if answer == 'n' or answer == 'no': new_path = input(f"Enter the path for {key}: ") value['path'] = new_path.strip() inputs[key] = {"filename": Path(value['path']).name}