Merge pull request #2668 from mashehu/fix-modules-list-json

Modules: Fix empty json output for `nf-core modules list local`

CHANGELOG.md

@@ -16,12 +16,13 @@
 
 ### Linting
 
+- Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))
 - linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
 - environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
 
 ### Modules
 
-- Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))
+- Fix empty json output for `nf-core list local` ([#2668](https://github.com/nf-core/tools/pull/2668))
 
 ### Subworkflows
 

nf_core/components/list.py

@@ -70,7 +70,7 @@ def pattern_msg(keywords: List[str]) -> str:
         # We have a pipeline - list what's installed
         else:
             # Check that we are in a pipeline directory
-
+            print(f"{self.repo_type=}")
             try:
                 if self.repo_type != "pipeline":
                     raise UserWarning(
@@ -141,6 +141,7 @@ def pattern_msg(keywords: List[str]) -> str:
                             date = "[red]Not Available"
                             message = "[red]Not Available"
                         table.add_row(component, repo_url, version_sha, message, date)
+                        components.append(component)
 
         if print_json:
             return json.dumps(components, sort_keys=True, indent=4)

tests/modules/list.py

@@ -1,3 +1,7 @@
+import json
+from pathlib import Path
+
+import yaml
 from rich.console import Console
 
 import nf_core.modules
@@ -56,3 +60,75 @@ def test_modules_install_gitlab_and_list_pipeline(self):
     console.print(listed_mods)
     output = console.export_text()
     assert "fastqc" in output
+
+
+def test_modules_list_local_json(self):
+    """Test listing locally installed modules as JSON"""
+    mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+    listed_mods = mods_list.list_components(print_json=True)
+    listed_mods = json.loads(listed_mods)
+    assert "fastqc" in listed_mods
+    assert "multiqc" in listed_mods
+
+
+def test_modules_list_remote_json(self):
+    """Test listing available modules as JSON"""
+    mods_list = nf_core.modules.ModuleList(None, remote=True)
+    listed_mods = mods_list.list_components(print_json=True)
+    listed_mods = json.loads(listed_mods)
+    assert "fastqc" in listed_mods
+    assert "multiqc" in listed_mods
+
+
+def test_modules_list_with_one_keyword(self):
+    """Test listing available modules with one keyword"""
+    mods_list = nf_core.modules.ModuleList(None, remote=True)
+    listed_mods = mods_list.list_components(keywords=["qc"])
+    console = Console(record=True)
+    console.print(listed_mods)
+    output = console.export_text()
+    assert "multiqc" in output
+
+
+def test_modules_list_with_keywords(self):
+    """Test listing available modules with multiple keywords"""
+    mods_list = nf_core.modules.ModuleList(None, remote=True)
+    listed_mods = mods_list.list_components(keywords=["fastq", "qc"])
+    console = Console(record=True)
+    console.print(listed_mods)
+    output = console.export_text()
+    assert "fastqc" in output
+
+
+def test_modules_list_with_unused_keyword(self):
+    """Test listing available modules with an unused keyword"""
+    mods_list = nf_core.modules.ModuleList(None, remote=True)
+    with self.assertLogs(level="INFO") as log:
+        listed_mods = mods_list.list_components(keywords=["you_will_never_find_me"])
+        self.assertIn("No available", log.output[0])
+        # expect empty list
+        assert listed_mods == ""
+
+
+def test_modules_list_in_wrong_repo_fail(self):
+    """Test listing available modules in a non-pipeline repo"""
+    # modify repotype in .nf-core.yml
+    with open(Path(self.pipeline_dir, ".nf-core.yml")) as fh:
+        nf_core_yml = yaml.safe_load(fh)
+    nf_core_yml_orig = nf_core_yml.copy()
+    nf_core_yml["repository_type"] = "modules"
+    nf_core_yml["org_path"] = "nf-core"
+
+    print(nf_core_yml)
+    with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh:
+        yaml.safe_dump(nf_core_yml, fh)
+    # expect error logged
+    with self.assertLogs(level="ERROR") as log:
+        mods_list = nf_core.modules.ModuleList(self.pipeline_dir, remote=False)
+        listed_mods = mods_list.list_components()
+        self.assertIn("must be run from a pipeline directory", log.output[0])
+        # expect empty list
+        assert listed_mods == ""
+    # restore .nf-core.yml
+    with open(Path(self.pipeline_dir, ".nf-core.yml"), "w") as fh:
+        yaml.safe_dump(nf_core_yml_orig, fh)

tests/test_modules.py

@@ -212,9 +212,15 @@ def test_modulesrepo_class(self):
     from .modules.list import (  # type: ignore[misc]
         test_modules_install_and_list_pipeline,
         test_modules_install_gitlab_and_list_pipeline,
+        test_modules_list_in_wrong_repo_fail,
+        test_modules_list_local_json,
         test_modules_list_pipeline,
         test_modules_list_remote,
         test_modules_list_remote_gitlab,
+        test_modules_list_remote_json,
+        test_modules_list_with_keywords,
+        test_modules_list_with_one_keyword,
+        test_modules_list_with_unused_keyword,
     )
     from .modules.modules_json import (  # type: ignore[misc]
         test_get_modules_json,