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Remove duplicate code #2053

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Merged
awgymer merged 3 commits into from
Nov 25, 2022
Merged

Remove duplicate code #2053

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9668478
Replace calls from specific functions to generalised get_all_components
awgymer Nov 24, 2022
cacb62e
Remove unused functions
awgymer Nov 24, 2022
d78abd9
Simplify redundant statement and move magic methods to top of class
awgymer Nov 25, 2022
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7 changes: 3 additions & 4 deletions nf_core/components/components_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,10 +80,9 @@ def _check_inputs(self):
else:
modules_json = ModulesJson(self.dir)
modules_json.check_up_to_date()
if self.component_type == "modules":
installed_components = modules_json.get_all_modules().get(self.modules_repo.remote_url)
elif self.component_type == "subworkflows":
modules_json.get_installed_subworkflows().get(self.modules_repo.remote_url)
installed_components = modules_json.get_all_components(self.component_type).get(
self.modules_repo.remote_url
)

# Get the component name if not specified
if self.component_name is None:
Expand Down
2 changes: 1 addition & 1 deletion nf_core/modules/lint/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ def __init__(
if self.repo_type == "pipeline":
modules_json = ModulesJson(self.dir)
modules_json.check_up_to_date()
all_pipeline_modules = modules_json.get_all_modules()
all_pipeline_modules = modules_json.get_all_components(self.component_type)
if self.modules_repo.remote_url in all_pipeline_modules:
module_dir = Path(self.dir, "modules", "nf-core")
self.all_remote_modules = [
Expand Down
54 changes: 8 additions & 46 deletions nf_core/modules/modules_json.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,14 @@ def __init__(self, pipeline_dir):
self.pipeline_subworkflows = None
self.pipeline_components = None

def __str__(self):
if self.modules_json is None:
self.load()
return json.dumps(self.modules_json, indent=4)

def __repr__(self):
return self.__str__()

def create(self):
"""
Creates the modules.json file from the modules and subworkflows installed in the pipeline directory
Expand Down Expand Up @@ -885,25 +893,6 @@ def get_subworkflow_version(self, subworkflow_name, repo_url, install_dir):
.get("git_sha", None)
)

def get_all_modules(self):
"""
Retrieves all pipeline modules that are reported in the modules.json

Returns:
(dict[str, [(str, str)]]): Dictionary indexed with the repo urls, with a
list of tuples (module_dir, module) as values
"""
if self.modules_json is None:
self.load()
if self.pipeline_modules is None:
self.pipeline_modules = {}
for repo, repo_entry in self.modules_json.get("repos", {}).items():
if "modules" in repo_entry:
for dir, modules in repo_entry["modules"].items():
self.pipeline_modules[repo] = [(dir, m) for m in modules]

return self.pipeline_modules

def get_all_components(self, component_type):
"""
Retrieves all pipeline modules/subworkflows that are reported in the modules.json
Expand Down Expand Up @@ -1004,33 +993,6 @@ def dump(self):
json.dump(self.modules_json, fh, indent=4)
fh.write("\n")

def __str__(self):
if self.modules_json is None:
self.load()
return json.dumps(self.modules_json, indent=4)

def __repr__(self):
return self.__str__()

def get_installed_subworkflows(self):
"""
Retrieves all pipeline subworkflows that are reported in the modules.json

Returns:
(dict[str, [(str, str)]]): Dictionary indexed with the repo urls, with a
list of tuples (module_dir, subworkflow) as values
"""
if self.modules_json is None:
self.load()
if self.pipeline_subworkflows is None:
self.pipeline_subworkflows = {}
for repo, repo_entry in self.modules_json.get("repos", {}).items():
if "subworkflows" in repo_entry:
for dir, subworkflow in repo_entry["subworkflows"].items():
self.pipeline_subworkflows[repo] = [(dir, name) for name in subworkflow]

return self.pipeline_subworkflows

def resolve_missing_installation(self, missing_installation, component_type):
missing_but_in_mod_json = [
f"'{component_type}/{install_dir}/{component}'"
Expand Down
4 changes: 2 additions & 2 deletions nf_core/modules/patch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ def param_check(self, module):
if not self.has_valid_directory():
raise UserWarning()

modules = self.modules_json.get_all_modules()[self.modules_repo.remote_url]
modules = self.modules_json.get_all_components(self.component_type)[self.modules_repo.remote_url]
module_names = [module for _, module in modules]

if module is not None and module not in module_names:
Expand All @@ -38,7 +38,7 @@ def patch(self, module=None):

self.modules_json.check_up_to_date()
self.param_check(module)
modules = self.modules_json.get_all_modules()[self.modules_repo.remote_url]
modules = self.modules_json.get_all_components(self.component_type)[self.modules_repo.remote_url]

if module is None:
choices = [module if dir == "nf-core" else f"{dir}/{module}" for dir, module in modules]
Expand Down