added tests

tests/subworkflows/patch.py

@@ -1,5 +1,28 @@
 import os
+import tempfile
 from pathlib import Path
+from unittest import mock
+
+
+import pytest
+
+from nf_core.modules.modules_json import ModulesJson
+from nf_core.subworkflows.install import SubworkflowInstall
+import nf_core.subworkflows
+import nf_core.components.components_command
+
+
+from ..utils import (
+    GITLAB_BRANCH_TEST_BRANCH,
+    GITLAB_REPO,
+    GITLAB_SUBWORKFLOWS_BRANCH,
+    GITLAB_SUBWORKFLOWS_ORG_PATH_BRANCH,
+    GITLAB_URL,
+    with_temporary_folder,
+)
+
+# TODO: #Change this for the correct SUCCEED_SHA
+SUCCEED_SHA = "????"
 
 """
 Test the 'nf-core subworkflows patch' command
@@ -30,29 +53,123 @@ def modify_subworkflow(path):
         fh.writelines(lines)
 
 
-def test_create_patch_change(self):
+def test_create_patch_no_change(self):
     """Test creating a patch when there is a change to the module"""
+    setup_patch(self.pipeline_dir, False)
 
+    # Try creating a patch file
+    patch_obj = nf_core.subworkflows.SubworkflowPatch(self.pipeline_dir, GITLAB_URL, GITLAB_BRANCH_TEST_BRANCH)
+    with pytest.raises(UserWarning):
+        patch_obj.patch("bam_sort_stats_samtools")
 
-def test_create_patch_no_change(self):
+    subworkflow_path = Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_sort_stats_samtools")
+
+    # Check that no patch file has been added to the directory
+    assert set(os.listdir(subworkflow_path)) == {"main.nf", "meta.yml"}
+
+def test_create_patch_change(self):
     """Test creating a patch when there is no change to the subworkflow"""
+    setup_patch(self.pipeline_dir, True)
+
     # Try creating a patch file
-    # Check that no patch file has been added to the directory
+    patch_obj = nf_core.subworkflows.SubworkflowPatch(self.pipeline_dir, GITLAB_URL, GITLAB_BRANCH_TEST_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
 
+    subworkflow_path = Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_sort_stats_samtools")
 
-def test_create_patch_try_apply_failed(self):
-    """Test creating a patch file and applying it to a new version of the the files"""
+    patch_fn = f"{'-'.join("bam_sort_stats_samtools".split('/'))}.diff"
+    # Check that a patch file with the correct name has been created
+    assert set(os.listdir(subworkflow_path)) == {"main.nf", "meta.yml", patch_fn}
+
+    # Check that the correct lines are in the patch file
+    with open(subworkflow_path / patch_fn) as fh:
+        patch_lines = fh.readlines()
+    subworkflow_relpath = subworkflow_path.relative_to(self.pipeline_dir)
+    assert f"--- {subworkflow_relpath / 'main.nf'}\n" in patch_lines, subworkflow_relpath / "main.nf"
+    assert f"+++ {subworkflow_relpath / 'main.nf'}\n" in patch_lines
+    assert "-    ch_fasta // channel: [ val(meta), path(fasta) ]" in patch_lines
 
 
 def test_create_patch_try_apply_successful(self):
     """Test creating a patch file and applying it to a new version of the the files"""
+    setup_patch(self.pipeline_dir, True)
+    subworkflow_relpath = Path("subworkflows", "nf-core", "bam_sort_stats_samtools")
+    subworkflow_path = Path(self.pipeline_dir, subworkflow_relpath)
 
+    # Try creating a patch file
+    patch_obj = nf_core.subworkflows.SubworkflowPatch(self.pipeline_dir, GITLAB_URL, GITLAB_BRANCH_TEST_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
+
+    patch_fn = f"{'-'.join("bam_sort_stats_samtools".split('/'))}.diff"
+    # Check that a patch file with the correct name has been created
+    assert set(os.listdir(subworkflow_path)) == {"main.nf", "meta.yml", patch_fn}
+
+    update_obj = nf_core.subworkflows.SubworkflowUpdate(
+        self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH
+    )
+
+    # Install the new files
+    install_dir = Path(tempfile.mkdtemp())
+    update_obj.install_component_files("bam_sort_stats_samtools", SUCCEED_SHA, update_obj.modules_repo, install_dir)
+
+    # Try applying the patch
+    subworkflow_install_dir = install_dir / "bam_sort_stats_samtools"
+    patch_relpath = subworkflow_relpath / patch_fn
+    assert update_obj.try_apply_patch("bam_sort_stats_samtools", "nf-core", patch_relpath, subworkflow_path, subworkflow_install_dir) is True
+
+    # Move the files from the temporary directory
+    update_obj.move_files_from_tmp_dir("bam_sort_stats_samtools", install_dir, "nf-core", SUCCEED_SHA)
+
+    # Check that a patch file with the correct name has been created
+    assert set(os.listdir(subworkflow_path)) == {"main.nf", "meta.yml", patch_fn}
+
+    # Check that the correct lines are in the patch file
+    with open(subworkflow_path / patch_fn) as fh:
+        patch_lines = fh.readlines()
+    subworkflow_relpath = subworkflow_path.relative_to(self.pipeline_dir)
+    assert f"--- {subworkflow_relpath / 'main.nf'}\n" in patch_lines, subworkflow_relpath / "main.nf"
+    assert f"+++ {subworkflow_relpath / 'main.nf'}\n" in patch_lines
+    assert "-    ch_fasta // channel: [ val(meta), path(fasta) ]" in patch_lines
+
+    # Check that 'main.nf' is updated correctly
+    with open(subworkflow_path / "main.nf") as fh:
+        main_nf_lines = fh.readlines()
+    # These lines should have been removed by the patch
+    assert "    ch_fasta // channel: [ val(meta), path(fasta) ]\n" not in main_nf_lines
 
-def test_create_patch_update_fail(self):
-    """Test creating a patch file and updating a subworkflow when there is a diff conflict"""
+def test_create_patch_try_apply_failed(self):
+    """Test creating a patch file and applying it to a new version of the the files"""
+    setup_patch(self.pipeline_dir, True)
+    subworkflow_relpath = Path("subworkflows", "nf-core", "bam_sort_stats_samtools")
+    subworkflow_path = Path(self.pipeline_dir, subworkflow_relpath)
+
+    # Try creating a patch file
+    patch_obj = nf_core.subworkflows.SubworkflowPatch(self.pipeline_dir, GITLAB_URL, GITLAB_BRANCH_TEST_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
+
+    patch_fn = f"{'-'.join("bam_sort_stats_samtools".split('/'))}.diff"
+    # Check that a patch file with the correct name has been created
+    assert set(os.listdir(subworkflow_path)) == {"main.nf", "meta.yml", patch_fn}
+
+    update_obj = nf_core.subworkflows.SubworkflowUpdate(
+        self.pipeline_dir, sha=SUCCEED_SHA, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH
+    )
 
+    # Install the new files
+    install_dir = Path(tempfile.mkdtemp())
+    update_obj.install_component_files("bam_sort_stats_samtools", SUCCEED_SHA, update_obj.modules_repo, install_dir)
 
+    # Try applying the patch
+    subworkflow_install_dir = install_dir / "bam_sort_stats_samtools"
+    patch_relpath = subworkflow_relpath / patch_fn
+    assert update_obj.try_apply_patch("bam_sort_stats_samtools", "nf-core", patch_relpath, subworkflow_path, subworkflow_install_dir) is False
+
+# TODO: create those two missing tests
 def test_create_patch_update_success(self):
+    """Test creating a patch file and updating a subworkflow when there is a diff conflict"""
+
+
+def test_create_patch_update_fail(self):
     """
     Test creating a patch file and the updating the subworkflow
 
@@ -63,3 +180,21 @@ def test_create_patch_update_success(self):
 
 def test_remove_patch(self):
     """Test creating a patch when there is no change to the subworkflow"""
+    setup_patch(self.pipeline_dir, True)
+
+    # Try creating a patch file
+    patch_obj = nf_core.subworkflows.SubworkflowPatch(self.pipeline_dir, GITLAB_URL, GITLAB_BRANCH_TEST_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
+
+    subworkflow_path = Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_sort_stats_samtools")
+
+    patch_fn = f"{'-'.join("bam_sort_stats_samtools".split('/'))}.diff"
+    # Check that a patch file with the correct name has been created
+    assert set(os.listdir(subworkflow_path)) == {"main.nf", "meta.yml", patch_fn}
+
+    with mock.patch.object(nf_core.create.questionary, "confirm") as mock_questionary:
+        mock_questionary.unsafe_ask.return_value = True
+        patch_obj.remove("bam_sort_stats_samtools")
+    # Check that the diff file has been removed
+    assert set(os.listdir(subworkflow_path)) == {"main.nf", "meta.yml"}
+