Merge pull request #2228 from anoronh4/feature/warn_multiple_remotes

Log error when multiple remotes have the same org name

.github/workflows/create-lint-wf.yml

@@ -107,15 +107,25 @@ jobs:
       - name: nf-core modules install
         run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
 
-      - name: nf-core modules install gitlab
-        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch main install fastqc --force --dir nf-core-testpipeline/
-
       - name: nf-core modules list local
         run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
 
       - name: nf-core modules list remote
         run: nf-core --log-file log.txt modules list remote
 
+      - name: nf-core modules remove
+        run: |
+          find nf-core-testpipeline/workflows/ -type f -exec sed -i '/^include /d' {} \;
+          nf-core --log-file log.txt modules remove fastqc --dir nf-core-testpipeline/
+          nf-core --log-file log.txt modules remove multiqc --dir nf-core-testpipeline/
+          nf-core --log-file log.txt modules remove custom/dumpsoftwareversions --dir nf-core-testpipeline/
+
+      - name: nf-core modules install gitlab
+        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch main install fastqc --force --dir nf-core-testpipeline/
+
+      - name: nf-core modules list local gitlab
+        run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
+
       - name: nf-core modules list remote gitlab
         run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote
 

CHANGELOG.md

@@ -39,6 +39,7 @@
 - Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to `nextflow.config`) ([#2196](https://github.com/nf-core/tools/pull/2196))
 - Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
 - Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).
+- Add warning when installing a module from an `org_path` that exists in multiple remotes in `modules.json` ([#2228](https://github.com/nf-core/tools/pull/2228)).
 
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 

nf_core/components/install.py

@@ -58,6 +58,12 @@ def install(self, component, silent=False):
         if not silent:
             modules_json.check_up_to_date()
 
+        # Verify that the remote repo's org_path does not match the org_path of any alternate repo among the installed modules
+        if self.check_alternate_remotes(modules_json):
+            err_msg = f"You are trying to install {self.component_type} from different repositories with the same organization name '{self.modules_repo.repo_path}' (set in the `.nf-core.yml` file in the `org_path` field).\nThis is not supported, and will likely cause problems. org_path should be set to the github account/organization name."
+            log.error(err_msg)
+            return False
+
         # Verify SHA
         if not self.modules_repo.verify_sha(self.prompt, self.sha):
             return False
@@ -264,3 +270,20 @@ def clean_modules_json(self, component, modules_repo, modules_json):
                             self.component_type, component, repo_to_remove, modules_repo.repo_path
                         )
                         return component_values["installed_by"]
+
+    def check_alternate_remotes(self, modules_json):
+        """
+        Check whether there are previously installed components with the same org_path but different remote urls
+        Log error if multiple remotes exist.
+
+        Return:
+            True: if problematic components are found
+            False: if problematic components are not found
+        """
+        modules_json.load()
+        for repo_url, repo_content in modules_json.modules_json.get("repos", dict()).items():
+            for component_type in repo_content:
+                for dir in repo_content.get(component_type, dict()).keys():
+                    if dir == self.modules_repo.repo_path and repo_url != self.modules_repo.remote_url:
+                        return True
+        return False

tests/modules/install.py

@@ -9,6 +9,7 @@
     GITLAB_BRANCH_TEST_BRANCH,
     GITLAB_REPO,
     GITLAB_URL,
+    remove_template_modules,
     with_temporary_folder,
 )
 
@@ -49,6 +50,7 @@ def test_modules_install_trimgalore_twice(self):
 
 def test_modules_install_from_gitlab(self):
     """Test installing a module from GitLab"""
+    remove_template_modules(self)
     assert self.mods_install_gitlab.install("fastqc") is True
 
 
@@ -61,6 +63,7 @@ def test_modules_install_different_branch_fail(self):
 
 def test_modules_install_different_branch_succeed(self):
     """Test installing a module from a different branch"""
+    remove_template_modules(self)
     install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
     # The fastp module does exists in the branch-test branch
     assert install_obj.install("fastp") is True
@@ -83,3 +86,10 @@ def test_modules_install_tracking(self):
     assert mod_json["repos"]["https://github.com/nf-core/modules.git"]["modules"]["nf-core"]["trimgalore"][
         "installed_by"
     ] == ["modules"]
+
+
+def test_modules_install_alternate_remote(self):
+    """Test installing a module from a different remote with the same organization path"""
+    install_obj = ModuleInstall(self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_BRANCH_TEST_BRANCH)
+    # The fastp module does exists in the branch-test branch
+    assert install_obj.install("fastp") is False

tests/modules/lint.py

@@ -5,7 +5,7 @@
 
 import nf_core.modules
 
-from ..utils import GITLAB_URL, set_wd
+from ..utils import GITLAB_URL, remove_template_modules, set_wd
 from .patch import BISMARK_ALIGN, CORRECT_SHA, PATCH_BRANCH, REPO_NAME, modify_main_nf
 
 
@@ -62,6 +62,7 @@ def test_modules_lint_no_gitlab(self):
 
 def test_modules_lint_gitlab_modules(self):
     """Lint modules from a different remote"""
+    remove_template_modules(self)
     self.mods_install_gitlab.install("fastqc")
     self.mods_install_gitlab.install("multiqc")
     module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
@@ -73,7 +74,7 @@ def test_modules_lint_gitlab_modules(self):
 
 def test_modules_lint_multiple_remotes(self):
     """Lint modules from a different remote"""
-    self.mods_install.install("fastqc")
+    remove_template_modules(self)
     self.mods_install_gitlab.install("multiqc")
     module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
     module_lint.lint(print_results=False, all_modules=True)
@@ -86,6 +87,7 @@ def test_modules_lint_patched_modules(self):
     """
     Test creating a patch file and applying it to a new version of the the files
     """
+    remove_template_modules(self)
     setup_patch(self.pipeline_dir, True)
 
     # Create a patch file

tests/modules/patch.py

@@ -7,7 +7,7 @@
 import nf_core.components.components_command
 import nf_core.modules
 
-from ..utils import GITLAB_URL
+from ..utils import GITLAB_URL, remove_template_modules
 
 """
 Test the 'nf-core modules patch' command
@@ -26,7 +26,7 @@
 REPO_URL = "https://gitlab.com/nf-core/modules-test.git"
 
 
-def setup_patch(pipeline_dir, modify_module):
+def setup_patch(pipeline_dir, modify_module, pipeline_name):
     install_obj = nf_core.modules.ModuleInstall(
         pipeline_dir, prompt=False, force=False, remote_url=GITLAB_URL, branch=PATCH_BRANCH, sha=ORG_SHA
     )
@@ -40,6 +40,15 @@ def setup_patch(pipeline_dir, modify_module):
         modify_main_nf(module_path / "main.nf")
 
 
+def modify_workflow_nf(path):
+    with open(path, "r") as fh:
+        lines = fh.readlines()
+    with open(path, "w") as fh:
+        for line in lines:
+            if not line.startswith("include {"):
+                fh.write(line)
+
+
 def modify_main_nf(path):
     """Modify a file to test patch creation"""
     with open(path, "r") as fh:
@@ -60,7 +69,10 @@ def modify_main_nf(path):
 
 def test_create_patch_no_change(self):
     """Test creating a patch when there is no change to the module"""
-    setup_patch(self.pipeline_dir, False)
+    # Remove modules that may cause org_path conflict
+    remove_template_modules(self)
+
+    setup_patch(self.pipeline_dir, False, self.pipeline_name)
 
     # Try creating a patch file
     patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
@@ -79,7 +91,10 @@ def test_create_patch_no_change(self):
 
 def test_create_patch_change(self):
     """Test creating a patch when there is a change to the module"""
-    setup_patch(self.pipeline_dir, True)
+    # Remove modules that may cause org_path conflict
+    remove_template_modules(self)
+
+    setup_patch(self.pipeline_dir, True, self.pipeline_name)
 
     # Try creating a patch file
     patch_obj = nf_core.modules.ModulePatch(self.pipeline_dir, GITLAB_URL, PATCH_BRANCH)
@@ -112,7 +127,10 @@ 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)
+    # Remove modules that may cause org_path conflict
+    remove_template_modules(self)
+
+    setup_patch(self.pipeline_dir, True, self.pipeline_name)
     module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN)
     module_path = Path(self.pipeline_dir, module_relpath)
 
@@ -178,7 +196,10 @@ 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)
+    # Remove modules that may cause org_path conflict
+    remove_template_modules(self)
+
+    setup_patch(self.pipeline_dir, True, self.pipeline_name)
     module_relpath = Path("modules", REPO_NAME, BISMARK_ALIGN)
     module_path = Path(self.pipeline_dir, module_relpath)
 
@@ -216,7 +237,10 @@ def test_create_patch_update_success(self):
     Should have the same effect as 'test_create_patch_try_apply_successful'
     but uses higher level api
     """
-    setup_patch(self.pipeline_dir, True)
+    # Remove modules that may cause org_path conflict
+    remove_template_modules(self)
+
+    setup_patch(self.pipeline_dir, True, self.pipeline_name)
     module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
 
     # Try creating a patch file
@@ -277,7 +301,10 @@ def test_create_patch_update_fail(self):
     """
     Test creating a patch file and updating a module when there is a diff conflict
     """
-    setup_patch(self.pipeline_dir, True)
+    # Remove modules that may cause org_path conflict
+    remove_template_modules(self)
+
+    setup_patch(self.pipeline_dir, True, self.pipeline_name)
     module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN)
 
     # Try creating a patch file

tests/modules/remove.py

@@ -1,5 +1,7 @@
 import os
 
+from ..utils import remove_template_modules
+
 
 def test_modules_remove_trimgalore(self):
     """Test removing TrimGalore! module after installing it"""
@@ -16,6 +18,9 @@ def test_modules_remove_trimgalore_uninstalled(self):
 
 def test_modules_remove_multiqc_from_gitlab(self):
     """Test removing multiqc module after installing it from an alternative source"""
+    # Remove modules that may cause org_path conflict
+    remove_template_modules(self)
+
     self.mods_install_gitlab.install("multiqc")
     module_path = os.path.join(self.mods_install_gitlab.dir, "modules", "nf-core", "multiqc")
     assert self.mods_remove_gitlab.remove("multiqc", force=True)

tests/modules/update.py

@@ -24,6 +24,7 @@
     GITLAB_URL,
     OLD_TRIMGALORE_BRANCH,
     OLD_TRIMGALORE_SHA,
+    remove_template_modules,
 )
 
 
@@ -44,6 +45,7 @@ def test_install_and_update(self):
 
 def test_install_at_hash_and_update(self):
     """Installs an old version of a module in the pipeline and updates it"""
+    remove_template_modules(self)
     assert self.mods_install_old.install("trimgalore")
     update_obj = ModuleUpdate(
         self.pipeline_dir, show_diff=False, update_deps=True, remote_url=GITLAB_URL, branch=OLD_TRIMGALORE_BRANCH
@@ -69,6 +71,7 @@ def test_install_at_hash_and_update(self):
 
 def test_install_at_hash_and_update_and_save_diff_to_file(self):
     """Installs an old version of a module in the pipeline and updates it"""
+    remove_template_modules(self)
     self.mods_install_old.install("trimgalore")
     patch_path = os.path.join(self.pipeline_dir, "trimgalore.patch")
     update_obj = ModuleUpdate(
@@ -109,6 +112,7 @@ def test_update_all(self):
 
 def test_update_with_config_fixed_version(self):
     """Try updating when there are entries in the .nf-core.yml"""
+    remove_template_modules(self)
     # Install trimgalore at the latest version
     assert self.mods_install_trimgalore.install("trimgalore")
 
@@ -134,6 +138,7 @@ def test_update_with_config_fixed_version(self):
 
 def test_update_with_config_dont_update(self):
     """Try updating when module is to be ignored"""
+    remove_template_modules(self)
     # Install an old version of trimgalore
     self.mods_install_old.install("trimgalore")
 
@@ -164,6 +169,7 @@ def test_update_with_config_dont_update(self):
 
 def test_update_with_config_fix_all(self):
     """Fix the version of all nf-core modules"""
+    remove_template_modules(self)
     self.mods_install_trimgalore.install("trimgalore")
 
     # Fix the version of all nf-core modules in the .nf-core.yml to an old version
@@ -187,6 +193,7 @@ def test_update_with_config_fix_all(self):
 
 def test_update_with_config_no_updates(self):
     """Don't update any nf-core modules"""
+    remove_template_modules(self)
     self.mods_install_old.install("trimgalore")
     old_mod_json = ModulesJson(self.pipeline_dir).get_modules_json()
 
@@ -220,6 +227,7 @@ def test_update_with_config_no_updates(self):
 
 def test_update_different_branch_single_module(self):
     """Try updating a module in a specific branch"""
+    remove_template_modules(self)
     install_obj = ModuleInstall(
         self.pipeline_dir,
         prompt=False,
@@ -246,6 +254,7 @@ def test_update_different_branch_single_module(self):
 
 def test_update_different_branch_mixed_modules_main(self):
     """Try updating all modules where MultiQC is installed from main branch"""
+    remove_template_modules(self)
     # Install fastp
     assert self.mods_install_gitlab_old.install("fastp")
 
@@ -272,6 +281,7 @@ def test_update_different_branch_mixed_modules_main(self):
 
 def test_update_different_branch_mix_modules_branch_test(self):
     """Try updating all modules where MultiQC is installed from branch-test branch"""
+    remove_template_modules(self)
     # Install multiqc from the branch-test branch
     assert self.mods_install_gitlab_old.install(
         "multiqc"

tests/subworkflows/install.py

@@ -10,6 +10,7 @@
     GITLAB_REPO,
     GITLAB_SUBWORKFLOWS_BRANCH,
     GITLAB_URL,
+    remove_template_modules,
     with_temporary_folder,
 )
 
@@ -62,6 +63,7 @@ def test_subworkflows_install_bam_sort_stats_samtools_twice(self):
 
 def test_subworkflows_install_from_gitlab(self):
     """Test installing a subworkflow from GitLab"""
+    remove_template_modules(self)
     assert self.subworkflow_install_gitlab.install("bam_stats_samtools") is True
     # Verify that the branch entry was added correctly
     modules_json = ModulesJson(self.pipeline_dir)
@@ -140,3 +142,9 @@ def test_subworkflows_install_tracking_added_super_subworkflow(self):
             "installed_by"
         ]
     ) == sorted(["subworkflows", "bam_sort_stats_samtools"])
+
+
+def test_subworkflows_install_alternate_remote(self):
+    """Test installing a subworkflow from a different remote with the same organization path"""
+    self.subworkflow_install.install("bam_sort_stats_samtools")
+    assert self.subworkflow_install_gitlab.install("bam_stats_samtools") is False

tests/subworkflows/list.py

@@ -2,7 +2,7 @@
 
 import nf_core.subworkflows
 
-from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL
+from ..utils import GITLAB_SUBWORKFLOWS_BRANCH, GITLAB_URL, remove_template_modules
 
 
 def test_subworkflows_list_remote(self):
@@ -40,6 +40,7 @@ def test_subworkflows_install_and_list_subworkflows(self):
 
 def test_subworkflows_install_gitlab_and_list_subworkflows(self):
     """Test listing locally installed subworkflows"""
+    remove_template_modules(self)
     self.subworkflow_install_gitlab.install("bam_sort_stats_samtools")
     subworkflows_list = nf_core.subworkflows.SubworkflowList(self.pipeline_dir, remote=False)
     listed_subworkflows = subworkflows_list.list_components()