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Merge pull request nf-core#3276 from mashehu/fix-create-params
handle new schema structure in `nf-core pipelines create-params-file`
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,79 +1,67 @@ | ||
| import json | ||
| import os | ||
| import shutil | ||
| import tempfile | ||
| from pathlib import Path | ||
|
|
||
| import nf_core.pipelines.create.create | ||
| import nf_core.pipelines.schema | ||
| from nf_core.pipelines.params_file import ParamsFileBuilder | ||
|
|
||
| from ..test_pipelines import TestPipelines | ||
|
|
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| class TestParamsFileBuilder: | ||
|
|
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| class TestParamsFileBuilder(TestPipelines): | ||
| """Class for schema tests""" | ||
|
|
||
| @classmethod | ||
| def setup_class(cls): | ||
| def setUp(self): | ||
| """Create a new PipelineSchema object""" | ||
| cls.schema_obj = nf_core.pipelines.schema.PipelineSchema() | ||
| cls.root_repo_dir = os.path.dirname(os.path.dirname(os.path.realpath(__file__))) | ||
|
|
||
| # Create a test pipeline in temp directory | ||
| cls.tmp_dir = tempfile.mkdtemp() | ||
| cls.template_dir = Path(cls.tmp_dir, "wf") | ||
| create_obj = nf_core.pipelines.create.create.PipelineCreate( | ||
| "testpipeline", "a description", "Me", outdir=cls.template_dir, no_git=True | ||
| ) | ||
| create_obj.init_pipeline() | ||
|
|
||
| cls.template_schema = Path(cls.template_dir, "nextflow_schema.json") | ||
| cls.params_template_builder = ParamsFileBuilder(cls.template_dir) | ||
| cls.invalid_template_schema = Path(cls.template_dir, "nextflow_schema_invalid.json") | ||
|
|
||
| # Remove the allOf section to make the schema invalid | ||
| with open(cls.template_schema) as fh: | ||
| o = json.load(fh) | ||
| del o["allOf"] | ||
|
|
||
| with open(cls.invalid_template_schema, "w") as fh: | ||
| json.dump(o, fh) | ||
|
|
||
| @classmethod | ||
| def teardown_class(cls): | ||
| if Path(cls.tmp_dir).exists(): | ||
| shutil.rmtree(cls.tmp_dir) | ||
| super().setUp() | ||
|
|
||
| self.template_schema = Path(self.pipeline_dir, "nextflow_schema.json") | ||
| self.params_template_builder = ParamsFileBuilder(self.pipeline_dir) | ||
| self.outfile = Path(self.pipeline_dir, "params-file.yml") | ||
|
|
||
| def test_build_template(self): | ||
| outfile = Path(self.tmp_dir, "params-file.yml") | ||
| self.params_template_builder.write_params_file(str(outfile)) | ||
| self.params_template_builder.write_params_file(self.outfile) | ||
|
|
||
| assert outfile.exists() | ||
| assert self.outfile.exists() | ||
|
|
||
| with open(outfile) as fh: | ||
| with open(self.outfile) as fh: | ||
| out = fh.read() | ||
|
|
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| assert "nf-core/testpipeline" in out | ||
|
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| def test_build_template_invalid_schema(self, caplog): | ||
| def test_build_template_invalid_schema(self): | ||
| """Build a schema from a template""" | ||
| outfile = Path(self.tmp_dir, "params-file-invalid.yml") | ||
| builder = ParamsFileBuilder(self.invalid_template_schema) | ||
| res = builder.write_params_file(str(outfile)) | ||
| schema = {} | ||
| with open(self.template_schema) as fh: | ||
| schema = json.load(fh) | ||
| del schema["allOf"] | ||
|
|
||
| with open(self.template_schema, "w") as fh: | ||
| json.dump(schema, fh) | ||
|
|
||
| builder = ParamsFileBuilder(self.template_schema) | ||
| res = builder.write_params_file(self.outfile) | ||
|
|
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| assert res is False | ||
| assert "Pipeline schema file is invalid" in caplog.text | ||
| assert "Pipeline schema file is invalid" in self.caplog.text | ||
|
|
||
| def test_build_template_file_exists(self, caplog): | ||
| def test_build_template_file_exists(self): | ||
| """Build a schema from a template""" | ||
|
|
||
| # Creates a new empty file | ||
| outfile = Path(self.tmp_dir) / "params-file.yml" | ||
| with open(outfile, "w"): | ||
| pass | ||
| self.outfile.touch() | ||
|
|
||
| res = self.params_template_builder.write_params_file(outfile) | ||
| res = self.params_template_builder.write_params_file(self.outfile) | ||
|
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| assert res is False | ||
| assert f"File '{outfile}' exists!" in caplog.text | ||
| assert f"File '{self.outfile}' exists!" in self.caplog.text | ||
|
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| self.outfile.unlink() | ||
|
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| outfile.unlink() | ||
| def test_build_template_content(self): | ||
| """Test that the content of the params file is correct""" | ||
| self.params_template_builder.write_params_file(self.outfile) | ||
|
|
||
| with open(self.outfile) as fh: | ||
| out = fh.read() | ||
|
|
||
| assert "nf-core/testpipeline" in out | ||
| assert "# input = null" in out |
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