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Specify yaml Loader argument #322

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Merged
phue merged 3 commits into from
Apr 28, 2019
Merged

Specify yaml Loader argument #322

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27b9669
Specify yaml Loader argument
phue Apr 23, 2019
025aca5
add Loader to remaining yaml.load() calls
phue Apr 23, 2019
8946dc9
use yaml.safe_load() to avoid unsafe loading of yaml
phue Apr 28, 2019
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@

#### Other
* Fix small typo in central readme of tools for future releases
* Switched to yaml.safe_load() to fix PyYAML warning that was thrown because of a possible [exploit](https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation)

## v1.6

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2 changes: 1 addition & 1 deletion nf_core/licences.py
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Expand Up @@ -44,7 +44,7 @@ def fetch_conda_licences(self):
raise LookupError("Couldn't find pipeline nf-core/{}".format(self.pipeline))

lint_obj = nf_core.lint.PipelineLint(self.pipeline)
lint_obj.conda_config = yaml.load(response.text)
lint_obj.conda_config = yaml.safe_load(response.text)
# Check conda dependency list
for dep in lint_obj.conda_config.get('dependencies', []):
try:
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4 changes: 2 additions & 2 deletions nf_core/lint.py
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Expand Up @@ -261,7 +261,7 @@ def pf(file_path):
# Load and parse files for later
if 'environment.yml' in self.files:
with open(os.path.join(self.path, 'environment.yml'), 'r') as fh:
self.conda_config = yaml.load(fh)
self.conda_config = yaml.safe_load(fh)

def check_docker(self):
"""Checks that Dockerfile contains the string ``FROM``."""
Expand Down Expand Up @@ -446,7 +446,7 @@ def check_ci_config(self):
fn = os.path.join(self.path, cf)
if os.path.isfile(fn):
with open(fn, 'r') as fh:
ciconf = yaml.load(fh)
ciconf = yaml.safe_load(fh)
# Check that we have the master branch protection
travisMasterCheck = '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
try:
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4 changes: 2 additions & 2 deletions tests/test_lint.py
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Expand Up @@ -260,7 +260,7 @@ def test_conda_env_pass(self):
lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
lint_obj.files = ['environment.yml']
with open(os.path.join(PATH_WORKING_EXAMPLE, 'environment.yml'), 'r') as fh:
lint_obj.conda_config = yaml.load(fh)
lint_obj.conda_config = yaml.safe_load(fh)
lint_obj.pipeline_name = 'tools'
lint_obj.config['manifest.version'] = '0.4'
lint_obj.check_conda_env_yaml()
Expand All @@ -272,7 +272,7 @@ def test_conda_env_fail(self):
lint_obj = nf_core.lint.PipelineLint(PATH_WORKING_EXAMPLE)
lint_obj.files = ['environment.yml']
with open(os.path.join(PATH_WORKING_EXAMPLE, 'environment.yml'), 'r') as fh:
lint_obj.conda_config = yaml.load(fh)
lint_obj.conda_config = yaml.safe_load(fh)
lint_obj.conda_config['dependencies'] = ['fastqc', 'multiqc=0.9', 'notapackaage=0.4']
lint_obj.pipeline_name = 'not_tools'
lint_obj.config['manifest.version'] = '0.23'
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