From dd2032d584e6b909812a36828531b4ce2f084035 Mon Sep 17 00:00:00 2001
From: Erik Danielsson <danielsson.erik.0@gmail.com>
Date: Tue, 2 Aug 2022 16:41:14 +0200
Subject: [PATCH] Fix failing tests

---
 nf_core/modules/lint/__init__.py |  5 ++++-
 nf_core/modules/lint/meta_yml.py |  2 +-
 tests/modules/lint.py            | 28 +++++++++++++++++++++++-----
 tests/test_modules.py            |  2 ++
 4 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
index 43d19419f3..e0e4374994 100644
--- a/nf_core/modules/lint/__init__.py
+++ b/nf_core/modules/lint/__init__.py
@@ -96,9 +96,12 @@ def __init__(self, dir, fail_warned=False, remote_url=None, branch=None, no_pull
             else:
                 raise LookupError(f"No modules from {self.modules_repo.remote_url} installed in pipeline.")
         else:
+            module_dir = Path(self.dir, "modules")
             self.all_remote_modules = [
-                NFCoreModule(module_dir / m, self.repo_type, Path(self.dir)) for m in self.module_names["modules"]
+                NFCoreModule(m, None, module_dir / m, self.repo_type, Path(self.dir))
+                for m in self.module_names["modules"]
             ]
+            self.all_local_modules = []
 
         self.lint_config = None
         self.modules_json = None
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 42f5ac21a1..146796fde2 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -28,7 +28,7 @@ def meta_yml(module_lint_object, module):
     if module.is_patched:
         lines = ModulesDiffer.try_apply_patch(
             module.module_name,
-            "nf-core/modules",
+            module_lint_object.modules_repo.fullname,
             module.patch_path,
             Path(module.module_dir).relative_to(module.base_dir),
             reverse=True,
diff --git a/tests/modules/lint.py b/tests/modules/lint.py
index 0f60377d5e..64b5f2ff0f 100644
--- a/tests/modules/lint.py
+++ b/tests/modules/lint.py
@@ -1,5 +1,9 @@
+import pytest
+
 import nf_core.modules
 
+from ..utils import GITLAB_URL
+
 
 def test_modules_lint_trimgalore(self):
     """Test linting the TrimGalore! module"""
@@ -16,11 +20,8 @@ def test_modules_lint_empty(self):
     self.mods_remove.remove("fastqc")
     self.mods_remove.remove("multiqc")
     self.mods_remove.remove("custom/dumpsoftwareversions")
-    module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
-    module_lint.lint(print_results=False, all_modules=True)
-    assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-    assert len(module_lint.passed) == 0
-    assert len(module_lint.warned) == 0
+    with pytest.raises(LookupError):
+        nf_core.modules.ModuleLint(dir=self.pipeline_dir)
 
 
 def test_modules_lint_new_modules(self):
@@ -30,3 +31,20 @@ def test_modules_lint_new_modules(self):
     assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
     assert len(module_lint.passed) > 0
     assert len(module_lint.warned) >= 0
+
+
+def test_modules_lint_no_gitlab(self):
+    """Test linting a pipeline with no modules installed"""
+    with pytest.raises(LookupError):
+        nf_core.modules.ModuleLint(dir=self.pipeline_dir, remote_url=GITLAB_URL)
+
+
+def test_modules_lint_gitlab_modules(self):
+    """Lint modules from a different remote"""
+    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)
+    module_lint.lint(print_results=False, all_modules=True)
+    assert len(module_lint.failed) == 0
+    assert len(module_lint.passed) > 0
+    assert len(module_lint.warned) >= 0
diff --git a/tests/test_modules.py b/tests/test_modules.py
index beb6c54abf..c3a9abfbf8 100644
--- a/tests/test_modules.py
+++ b/tests/test_modules.py
@@ -110,7 +110,9 @@ def test_modulesrepo_class(self):
     )
     from .modules.lint import (
         test_modules_lint_empty,
+        test_modules_lint_gitlab_modules,
         test_modules_lint_new_modules,
+        test_modules_lint_no_gitlab,
         test_modules_lint_trimgalore,
     )
     from .modules.list import (