added patch command for subworkflows

nf_core/__main__.py

@@ -1685,6 +1685,43 @@ def subworkflows_install(ctx, subworkflow, dir, prompt, force, sha):
         sys.exit(1)
 
 
+# nf-core subworkflows patch
+@subworkflows.command("patch")
+@click.pass_context
+@click.argument("tool", type=str, required=False, metavar="<tool> or <tool/subtool>")
+@click.option(
+    "-d",
+    "--dir",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory. [dim]\[default: current working directory][/]",
+)
+@click.option("-r", "--remove", is_flag=True, default=False)
+def subworkflows_patch(ctx, tool, dir, remove):
+    """
+    Create a patch file for minor changes in a subworkflow
+
+    Checks if a subworkflow has been modified locally and creates a patch file
+    describing how the module has changed from the remote version
+    """
+    from nf_core.subworkflows import SubworkflowPatch
+
+    try:
+        subworkflow_patch = SubworkflowPatch(
+            dir,
+            ctx.obj["modules_repo_url"],
+            ctx.obj["modules_repo_branch"],
+            ctx.obj["modules_repo_no_pull"],
+        )
+        if remove:
+            subworkflow_patch.remove(tool)
+        else:
+            subworkflow_patch.patch(tool)
+    except (UserWarning, LookupError) as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core subworkflows remove
 @subworkflows.command("remove")
 @click.pass_context

nf_core/subworkflows/__init__.py

@@ -3,5 +3,6 @@
 from .install import SubworkflowInstall
 from .lint import SubworkflowLint
 from .list import SubworkflowList
+from .patch import SubworkflowPatch
 from .remove import SubworkflowRemove
 from .update import SubworkflowUpdate

nf_core/subworkflows/patch.py

@@ -0,0 +1,10 @@
+import logging
+
+from nf_core.components.patch import ComponentPatch
+
+log = logging.getLogger(__name__)
+
+
+class SubworkflowPatch(ComponentPatch):
+    def __init__(self, pipeline_dir, remote_url=None, branch=None, no_pull=False, installed_by=False):
+        super().__init__(pipeline_dir, "subworkflows", remote_url, branch, no_pull, installed_by)

tests/subworkflows/patch.py

@@ -0,0 +1,212 @@
+import os
+import tempfile
+from pathlib import Path
+from unittest import mock
+
+import pytest
+
+import nf_core.components.components_command
+import nf_core.subworkflows
+
+from ..utils import (
+    GITLAB_SUBWORKFLOWS_BRANCH,
+    GITLAB_URL,
+    GITLAB_REPO
+)
+
+# TODO: #Change this for the correct SUCCEED_SHA
+SUCCEED_SHA = "????"
+ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2"
+
+
+"""
+Test the 'nf-core subworkflows patch' command
+"""
+
+
+def setup_patch(pipeline_dir, modify_subworkflow):
+    # Install the subworkflow bam_sort_stats_samtools
+    install_obj = nf_core.subworkflows.SubworkflowInstall(
+        pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=GITLAB_SUBWORKFLOWS_BRANCH, sha=ORG_SHA
+    )
+
+    # Install the module
+    install_obj.install("bam_sort_stats_samtools")
+
+    if modify_subworkflow:
+        # Modify the subworkflow
+        subworkflow_path = Path(pipeline_dir, "subworkflows", GITLAB_REPO, "bam_sort_stats_samtools")
+        modify_main_nf(subworkflow_path / "main.nf")
+
+
+def modify_main_nf(path):
+    """Modify a file to test patch creation"""
+    with open(path) as fh:
+        lines = fh.readlines()
+    # We want a patch file that looks something like:
+    # -    ch_fasta // channel: [ val(meta), path(fasta) ]
+    for line_index in range(len(lines)):
+        if lines[line_index] == "    ch_fasta // channel: [ val(meta), path(fasta) ]\n":
+            to_pop = line_index
+    lines.pop(to_pop)
+    with open(path, "w") as fh:
+        fh.writelines(lines)
+
+
+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_SUBWORKFLOWS_BRANCH)
+    with pytest.raises(UserWarning):
+        patch_obj.patch("bam_sort_stats_samtools")
+
+    subworkflow_path = Path(self.pipeline_dir, "subworkflows", GITLAB_REPO, "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
+    patch_obj = nf_core.subworkflows.SubworkflowPatch(self.pipeline_dir, GITLAB_URL, GITLAB_SUBWORKFLOWS_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
+
+    subworkflow_path = Path(self.pipeline_dir, "subworkflows", GITLAB_REPO, "bam_sort_stats_samtools")
+
+    patch_fn = f"{'-'.join('bam_sort_stats_samtools')}.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", GITLAB_REPO, "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_SUBWORKFLOWS_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
+
+    patch_fn = f"{'-'.join('bam_sort_stats_samtools')}.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_SUBWORKFLOWS_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", GITLAB_REPO, 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, GITLAB_REPO, 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_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", GITLAB_REPO, "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_SUBWORKFLOWS_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
+
+    patch_fn = f"{'-'.join('bam_sort_stats_samtools')}.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_SUBWORKFLOWS_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", GITLAB_REPO, 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
+
+    Should have the same effect as 'test_create_patch_try_apply_successful'
+    but uses higher level api
+    """
+
+
+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_SUBWORKFLOWS_BRANCH)
+    patch_obj.patch("bam_sort_stats_samtools")
+
+    subworkflow_path = Path(self.pipeline_dir, "subworkflows", GITLAB_REPO, "bam_sort_stats_samtools")
+
+    patch_fn = f"{'-'.join('bam_sort_stats_samtools')}.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"}

tests/test_subworkflows.py

@@ -138,6 +138,15 @@ def tearDown(self):
         test_subworkflows_list_remote,
         test_subworkflows_list_remote_gitlab,
     )
+    from .subworkflows.patch import (  # type: ignore[misc]
+        test_create_patch_change,
+        test_create_patch_no_change,
+        test_create_patch_try_apply_failed,
+        test_create_patch_try_apply_successful,
+        test_create_patch_update_fail,
+        test_create_patch_update_success,
+        test_remove_patch,
+    )
     from .subworkflows.remove import (  # type: ignore[misc]
         test_subworkflows_remove_included_subworkflow,
         test_subworkflows_remove_one_of_two_subworkflow,