Merge pull request #35 from qbic-pipelines/dev

fixed query-api-civic --cancer bug #33
bumped version to 0.5.1

.github/workflows/lint-code.yml

@@ -19,7 +19,7 @@ jobs:
 
       # Run editor config check only on files not covered by a linter
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
+        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile\|.obo')
 
   Prettier:
     runs-on: ubuntu-latest

.github/workflows/pytest.yml

@@ -28,7 +28,7 @@ jobs:
 
       - name: Install python dependencies
         run: |
-          python -m pip install --upgrade pip -r requirements-dev.txt
+          python -m pip install --upgrade pip -r requirements.txt
           pip install -e .
 
       - name: Test with pytest

CHANGELOG.rst

@@ -1,6 +1,20 @@
 Changelog
 ============
 
+0.5.1 - Sulfur Io  (2024-07-03)
+---------------------------------------------
+
+**Added**
+
+**Fixed**
+
+* fixed a severe bug in `query-api-civic` that made the tool unusable, the bug was introduced in v0.5.0.
+
+**Dependencies**
+
+**Deprecated**
+
+
 0.5.0 - Sulfur Io  (2024-06-23)
 ---------------------------------------------
 

LICENSE

@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-

README.rst

@@ -55,5 +55,3 @@ This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypack
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
 .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
-
-

example_files/cgi_test_out/cgi_test_out.cgi_results/cna_analysis.tsv

@@ -0,0 +1,4 @@
+internal_id	sample	gene	cna	cancer	predicted_in_tumors	gene_role	known_in_tumors	driver	driver_statement	predicted_match	known_match
+input01_1	test_1	ERBB2	AMP	CANCER	CESC;ESCA;HNSC;LUAD;PAAD;STAD;UCEC	Act	BRCA;OV;CANCER;NSCLC;ST;BT;COREAD;BLCA;GEJA;HNC;ED	known	known in: BRCA;OV;CANCER;NSCLC;ST;BT;COREAD;BLCA;GEJA;HNC;ED	known_match	known_match
+input01_2	test_1	TP53	DEL	CANCER	S	LoF	THYM;BCL	known	known in: THYM;BCL	known_match	known_match
+input01_3	test_1	EGFR	AMP	CANCER	BLCA;CESC;ESCA;LGG;LUAD;LUSC;STAD	Act	G;NSCLC;ED;HNSC;COREAD	known	known in: G;NSCLC;ED;HNSC;COREAD	known_match	known_match

querynator/__init__.py

@@ -1,5 +1,7 @@
 """Top-level package for querynator."""
 
-__author__ = """Susanne Jodoin & Mark Polster"""
-__email__ = "susanne.jodoin@qbic.uni-tuebingen.de | mark.polster@uni-tuebingen.de"
-__version__ = "0.5.0"
+__author__ = """Susanne Jodoin, Mark Polster & Niclas Grote"""
+__email__ = (
+    "susanne.jodoin@qbic.uni-tuebingen.de | mark.polster@uni-tuebingen.de | niclas.grote@student.uni-tuebingen.de"
+)
+__version__ = "0.5.1"

querynator/__main__.py

@@ -419,6 +419,13 @@ def query_api_cgi(mutations, cnas, translocations, cancer, genome, token, email,
     required=True,
     default="GRCh38",
 )
+@click.option(
+    "-c",
+    "--cancer",
+    help="the cancer DOID (id or name) to be searched.",
+    default=None,
+    type=click.STRING,
+)
 @click.option(
     "-f",
     "--filter_vep",
@@ -427,14 +434,7 @@ def query_api_cgi(mutations, cnas, translocations, cancer, genome, token, email,
     show_default=True,
     default=False,
 )
-@click.option(
-    "-c",
-    "--cancer",
-    help="the cancer DOID (id or name) to be searched.",
-    default=None,
-    type=click.STRING,
-)
-def query_api_civic(vcf, outdir, genome, cancer_doid, filter_vep):
+def query_api_civic(vcf, outdir, genome, cancer, filter_vep):
     try:
         result_dir = get_unique_querynator_dir(f"{outdir}")
         dirname, basename = os.path.split(result_dir)
@@ -447,7 +447,7 @@ def query_api_civic(vcf, outdir, genome, cancer_doid, filter_vep):
 
             logger.info("Query the Clinical Interpretations of Variants In Cancer (CIViC)")
             # run analysis
-            query_civic(candidate_variants, result_dir, logger, vcf, genome, cancer_doid, filter_vep)
+            query_civic(candidate_variants, result_dir, logger, vcf, genome, cancer, filter_vep)
 
         else:
             logger.info("Query the Clinical Interpretations of Variants In Cancer (CIViC)")

setup.py

@@ -18,8 +18,8 @@
 ]
 
 setup(
-    author="Susanne Jodoin, Mark Polster",
-    author_email="susanne.jodoin@qbic.uni-tuebingen.de, mark.polster@uni-tuebingen.de",
+    author="Susanne Jodoin, Mark Polster, Niclas Grote",
+    author_email="susanne.jodoin@qbic.uni-tuebingen.de, mark.polster@uni-tuebingen.de, niclas.grote@student.uni-tuebingen.de",
     python_requires=">=3.8,<3.11",
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
@@ -46,6 +46,6 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="https://github.com/qbic-pipelines/querynator",
-    version="0.5.0",
+    version="0.5.1",
     zip_safe=False,
 )

tests/test_querynator.py

@@ -2,50 +2,220 @@
 
 """Tests for `querynator` package."""
 
+import os
+import shutil
 import unittest
 
 from click.testing import CliRunner
 
-import querynator.__main__
+from querynator.__main__ import querynator_cli
 
 
-class testCLI(unittest.TestCase):
+class testCliHelp(unittest.TestCase):
+
+    def setUp(self):
+        self.runner = CliRunner()
 
     def test_commandLineInterface(self):
         """Test the CLI."""
-        runner = CliRunner()
-        result = runner.invoke(querynator.__main__.querynator_cli)
-        assert result.exit_code == 0
+        result = self.runner.invoke(querynator_cli)
+        self.assertEqual(result.exit_code, 0)
 
+    def test_helpMessage(self):
         """Test help message"""
-        help_result = runner.invoke(querynator.__main__.querynator_cli, ["--help"])
-        assert help_result.exit_code == 0
-        assert "--help     Show this message and exit." in help_result.output
+        help_result = self.runner.invoke(querynator_cli, ["--help"])
+        self.assertEqual(help_result.exit_code, 0)
+        self.assertIn("--help     Show this message and exit.", help_result.output)
+        self.assertNotIn("+++lalelu+++this is not part of the help message+++", help_result.output)
 
+    def test_CgiHelp(self):
         """Test CGI help message"""
-        cgi_help_result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-cgi", "--help"])
-        assert cgi_help_result.exit_code == 0
-        assert "--help                          Show this message and exit." in cgi_help_result.output
+        cgi_help_result = self.runner.invoke(querynator_cli, ["query-api-cgi", "--help"])
+        self.assertEqual(cgi_help_result.exit_code, 0)
+        self.assertIn("--help                          Show this message and exit.", cgi_help_result.output)
 
+    def test_CivicHelp(self):
         """Test CIVIC help message"""
-        civic_help_result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-civic", "--help"])
-        assert civic_help_result.exit_code == 0
-        assert "--help                          Show this message and exit." in civic_help_result.output
+        civic_help_result = self.runner.invoke(querynator_cli, ["query-api-civic", "--help"])
+        self.assertEqual(civic_help_result.exit_code, 0)
+        self.assertIn("--help                          Show this message and exit.", civic_help_result.output)
 
+    def test_CreatereportHelp(self):
         """Test CREATE-REPORT help message"""
-        civic_help_result = runner.invoke(querynator.__main__.querynator_cli, ["create-report", "--help"])
-        assert civic_help_result.exit_code == 0
-        assert "--help                 Show this message and exit." in civic_help_result.output
+        report_help_result = self.runner.invoke(querynator_cli, ["create-report", "--help"])
+        self.assertEqual(report_help_result.exit_code, 0)
+        self.assertIn("--help                 Show this message and exit.", report_help_result.output)
 
+    def test_nonExistingSubcommand(self):
         """Test non-existing subcommand"""
-        result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-clinvar"])
-        assert result.exit_code == 2
-        assert "No such command" in result.output
+        result = self.runner.invoke(querynator_cli, ["query-api-clinvar"])
+        self.assertEqual(result.exit_code, 2)
+        self.assertIn("No such command", result.output)
 
+    def test_nonExistingOption(self):
         """Test non-existing option"""
-        result = runner.invoke(querynator.__main__.querynator_cli, ["query-api-cgi", "--baz"])
-        assert result.exit_code == 2
-        assert "No such option" in result.output
+        result = self.runner.invoke(querynator_cli, ["query-api-cgi", "--baz"])
+        self.assertEqual(result.exit_code, 2)
+        self.assertIn("No such option", result.output)
+
+
+class testCliRun(unittest.TestCase):
+    unittest_dir = f"{os.getcwd()}/example_files/unittest_out"
+
+    # helper functions
+    def assertIsFile(self, path, msg=None):
+        msg = f"{path} is not a file" if msg is None else msg
+        self.assertTrue(os.path.isfile(path), msg)
+
+    def get_testdir(self):
+        """Get the test directory for the current test method."""
+        method_name = str(self).split()[0]
+        return f"{self.unittest_dir}/{method_name}"
+
+    def clean_testdir(self):
+        try:
+            shutil.rmtree(self.get_testdir())
+        except FileNotFoundError:
+            pass
+
+    # tests
+    def setUp(self):
+        self.runner = CliRunner()
+        self.clean_testdir()
+
+    def test_queryApiCivic(self):
+        """Test query-api-civic"""
+        outdir = self.get_testdir()
+        result = self.runner.invoke(
+            querynator_cli,
+            [
+                "query-api-civic",
+                "--vcf",
+                f"{os.getcwd()}/example_files/example.vcf",
+                "--genome",
+                "GRCh37",
+                "--outdir",
+                outdir,
+                "--filter_vep",
+            ],
+        )
+        self.assertEqual(result.exit_code, 0, "non-zero exit code")
+        self.assertIsFile(f"{outdir}/{outdir.split('/')[-1]}.civic_results.tsv", "civic_results.tsv not created")
+
+    def test_queryApiCivic_Cancer(self):
+        """Test query-api-civic"""
+        outdir = self.get_testdir()
+
+        result = self.runner.invoke(
+            querynator_cli,
+            [
+                "query-api-civic",
+                "--vcf",
+                "example_files/example.vcf",
+                "--genome",
+                "GRCh37",
+                "--outdir",
+                outdir,
+                "--cancer",
+                "Cholangiocarcinoma",
+                "--filter_vep",
+            ],
+        )
+        self.assertEqual(result.exit_code, 0, "non-zero exit code")
+        self.assertIsFile(f"{outdir}/{outdir.split('/')[-1]}.civic_results.tsv", "civic_results.tsv not created")
+
+    def test_queryApiCgi(self):
+        """test querynator query-api-cgi with dummy credentials"""
+        outdir = self.get_testdir()
+        result = self.runner.invoke(
+            querynator_cli,
+            [
+                "query-api-cgi",
+                "--mutations",
+                f"{os.getcwd()}/example_files/example.vcf",
+                "--genome",
+                "GRCh37",
+                "--outdir",
+                outdir,
+                "--email",
+                "dummy@internet.by",
+                "--token",
+                "thisisadummytoken",
+                "--filter_vep",
+            ],
+        )
+        self.assertEqual(result.exit_code, 1)
+
+    def test_queryApiCgi_Cancer(self):
+        """test querynator query-api-cgi with dummy credentials"""
+        outdir = self.get_testdir()
+        result = self.runner.invoke(
+            querynator_cli,
+            [
+                "query-api-cgi",
+                "--mutations",
+                f"{os.getcwd()}/example_files/example.vcf",
+                "--genome",
+                "GRCh37",
+                "--outdir",
+                outdir,
+                "--cancer",
+                "Breast adenocarcinoma",
+                "--email",
+                "dummy@internet.by",
+                "--token",
+                "thisisadummytoken",
+                "--filter_vep",
+            ],
+        )
+        self.assertEqual(result.exit_code, 1)
+
+    def test_queryApiCgi_invalidCancer(self):
+        """test querynator query-api-cgi with dummy credentials"""
+        outdir = self.get_testdir()
+        result = self.runner.invoke(
+            querynator_cli,
+            [
+                "query-api-cgi",
+                "--mutations",
+                f"{os.getcwd()}/example_files/example.vcf",
+                "--genome",
+                "GRCh37",
+                "--outdir",
+                outdir,
+                "--cancer",
+                "this is not cancer, 'tis but a flesh wound",
+                "--email",
+                "dummy@internet.by",
+                "--token",
+                "thisisadummytoken",
+                "--filter_vep",
+            ],
+        )
+        self.assertEqual(result.exit_code, 2)
+
+    def test_createReport(self):
+        """test querynator create-report on example files"""
+        outdir = self.get_testdir()
+        result = self.runner.invoke(
+            querynator_cli,
+            [
+                "create-report",
+                "--cgi_path",
+                f"{os.getcwd()}/example_files/cgi_test_out",
+                "--civic_path",
+                f"{os.getcwd()}/example_files/civic_test_out",
+                "--outdir",
+                outdir,
+            ],
+        )
+        self.assertEqual(result.exit_code, 0, "non-zero exit code")
+        self.assertIsFile(f"{outdir}/combined_files/civic_cgi_vep.tsv", "combined file not created")
+        self.assertIsFile(f"{outdir}/report/{outdir.split('/')[-1]}_overall_report.html", "report not created")
+
+    def tearDown(self):
+        """Clean up output directories after tests are run."""
+        self.clean_testdir()
 
 
 if __name__ == "__main__":