def test_validate_group_script_dir(self):
group_name = 'ENCODE-DCC'
script_group_dir = get_script_group_dir(group_name,
base_dir=self.test_content_dir)
validate_content(
[str(script_group_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_project_script_dir(self):
group_name = 'ENCODE-DCC'
project_name = 'atac-seq-pipeline'
script_project_dir = get_script_project_dir(
group_name, project_name, base_dir=self.test_content_dir)
validate_content(
[str(script_project_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_common_dir(self):
tool_name = 'md5sum'
version_name = '8.x'
common_dir = get_tool_common_dir(tool_name,
version_name,
base_dir=self.test_content_dir)
validate_content(
[str(common_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_tool_version_dir(self):
tool_name = 'samtools'
version_name = '1.x'
tool_version_dir = get_tool_version_dir(tool_name,
version_name,
base_dir=self.test_content_dir)
validate_content(
[str(tool_version_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_instance_dir(self):
tool_name = 'gawk'
version_name = '4.1.x'
subtool_name = None
instances_dir = get_tool_instances_dir(tool_name,
version_name,
subtool_name=subtool_name,
base_dir=self.test_content_dir)
validate_content(
[str(instances_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_main_subtool_dir(self):
tool_name = 'md5sum'
version_name = '8.x'
subtool_name = None
subtool_dir = get_tool_dir(tool_name,
version_name,
subtool_name,
base_dir=self.test_content_dir)
validate_content(
[str(subtool_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_script_dir(self):
group_name = 'ENCODE-DCC'
project_name = 'atac-seq-pipeline'
version_name = '1.1.x'
script_name = 'encode_ataqc'
script_dir = get_script_dir(group_name,
project_name,
version_name,
script_name,
base_dir=self.test_content_dir)
validate_content(
[str(script_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_script_instance_dir(self):
group_name = 'ENCODE-DCC'
project_name = 'atac-seq-pipeline'
version_name = '1.1.x'
script_name = 'encode_bam2ta' # No instances in there, but might as well have a test.
script_instance_dir = get_script_instance_dir(
group_name,
project_name,
version_name,
script_name,
base_dir=self.test_content_dir)
validate_content(
[str(script_instance_dir), '-p',
str(self.test_content_dir), '-q'])
return
def test_validate_main_tool_dir(self):
tool_name = 'STAR'
test_repo_path = self.test_content_dir
main_tool_dir = get_main_tool_dir(tool_name, base_dir=test_repo_path)
validate_content([str(main_tool_dir), '-p', str(test_repo_path), '-q'])
return