def test_module_resolver_with_mapping_specificity_rules():
# If a requirement demands a specific version,
# do not map to a different version when the version
# has not been specified explicitly
with __test_base_path() as temp_directory:
module_script = _setup_module_command(temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
blast/2.24
''')
mapping_file = os.path.join(temp_directory, "mapping")
with open(mapping_file, "w") as f:
f.write('''
- from:
name: blast
unversioned: true
to:
name: blast
version: 2.24
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
module = resolver.resolve(ToolRequirement(name="blast", type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.24", module.module_version # successful resolution, because Requirement does not ask for a specific version
module = resolver.resolve(ToolRequirement(name="blast", version="2.22", type="package"))
assert isinstance(module, NullDependency) # NullDependency, because we don't map `version: Null` over a Requirement that asks for a specific version
def test_module_resolver_with_mapping_specificity_rules():
# If a requirement demands a specific version,
# do not map to a different version when the version
# has not been specified explicitly
with __test_base_path() as temp_directory:
module_script = _setup_module_command(
temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
blast/2.24
''')
mapping_file = os.path.join(temp_directory, "mapping")
with open(mapping_file, "w") as f:
f.write('''
- from:
name: blast
unversioned: true
to:
name: blast
version: 2.24
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(),
modulecmd=module_script,
mapping_files=mapping_file)
module = resolver.resolve(ToolRequirement(name="blast",
type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.24", module.module_version # successful resolution, because Requirement does not ask for a specific version
module = resolver.resolve(
ToolRequirement(name="blast", version="2.22", type="package"))
assert isinstance(
module, NullDependency
) # NullDependency, because we don't map `version: Null` over a Requirement that asks for a specific version
def test_module_dependency_resolver():
with __test_base_path() as temp_directory:
module_script = _setup_module_command(temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
JAGS/3.2.0-gcc45
JAGS/3.3.0-gcc4.7.2
ProbABEL/0.1-3
ProbABEL/0.1-9e
R/2.12.2
R/2.13.1
R/2.14.1
R/2.15.0
R/2.15.1
R/3.0.1(default)
abokia-blast/2.0.2-130524/ompi_intel
abokia-blast/2.0.2-130630/ompi_intel
--------------------------- /soft/intel/modulefiles ----------------------------
advisor/2013/update1 intel/11.1.075 mkl/10.2.1.017
advisor/2013/update2 intel/11.1.080 mkl/10.2.5.035
advisor/2013/update3 intel/12.0 mkl/10.2.7.041
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script)
module = resolver.resolve(ToolRequirement(name="R", version=None, type="package"))
assert module.module_name == "R"
assert module.module_version is None
module = resolver.resolve(ToolRequirement(name="R", version="3.0.1", type="package"))
assert module.module_name == "R"
assert module.module_version == "3.0.1"
module = resolver.resolve(ToolRequirement(name="R", version="3.0.4", type="package"))
assert isinstance(module, NullDependency)
def test_module_dependency_resolver():
with __test_base_path() as temp_directory:
module_script = _setup_module_command(temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
JAGS/3.2.0-gcc45
JAGS/3.3.0-gcc4.7.2
ProbABEL/0.1-3
ProbABEL/0.1-9e
R/2.12.2
R/2.13.1
R/2.14.1
R/2.15.0
R/2.15.1
R/3.0.1(default)
abokia-blast/2.0.2-130524/ompi_intel
abokia-blast/2.0.2-130630/ompi_intel
--------------------------- /soft/intel/modulefiles ----------------------------
advisor/2013/update1 intel/11.1.075 mkl/10.2.1.017
advisor/2013/update2 intel/11.1.080 mkl/10.2.5.035
advisor/2013/update3 intel/12.0 mkl/10.2.7.041
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script)
module = resolver.resolve(ToolRequirement(name="R", version=None, type="package"))
assert module.module_name == "R"
assert module.module_version is None
module = resolver.resolve(ToolRequirement(name="R", version="3.0.1", type="package"))
assert module.module_name == "R"
assert module.module_version == "3.0.1"
module = resolver.resolve(ToolRequirement(name="R", version="3.0.4", type="package"))
assert isinstance(module, NullDependency)
def test_module_resolver_with_mapping_versions():
with __test_base_path() as temp_directory:
module_script = _setup_module_command(
temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
blast/2.22.0-mpi
blast/2.23
blast/2.24.0-mpi
''')
mapping_file = os.path.join(temp_directory, "mapping")
with open(mapping_file, "w") as f:
f.write('''
- from:
name: blast+
version: 2.24
to:
name: blast
version: 2.24.0-mpi
- from:
name: blast
version: 2.22
to:
version: 2.22.0-mpi
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(),
modulecmd=module_script,
mapping_files=mapping_file)
module = resolver.resolve(
ToolRequirement(name="blast+", version="2.24", type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.24.0-mpi", module.module_version
resolver = ModuleDependencyResolver(_SimpleDependencyManager(),
modulecmd=module_script,
mapping_files=mapping_file)
module = resolver.resolve(
ToolRequirement(name="blast+", version="2.23", type="package"))
assert isinstance(module, NullDependency)
module = resolver.resolve(
ToolRequirement(name="blast", version="2.22", type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.22.0-mpi", module.module_version
def test_module_dependency_resolver():
with __test_base_path() as temp_directory:
module_script = os.path.join(temp_directory, "modulecmd")
__write_script(
module_script, '''#!/bin/sh
cat %s/example_output 1>&2;
''' % temp_directory)
with open(os.path.join(temp_directory, "example_output"), "w") as f:
# Subset of module avail from MSI cluster.
f.write('''
-------------------------- /soft/modules/modulefiles ---------------------------
JAGS/3.2.0-gcc45
JAGS/3.3.0-gcc4.7.2
ProbABEL/0.1-3
ProbABEL/0.1-9e
R/2.12.2
R/2.13.1
R/2.14.1
R/2.15.0
R/2.15.1
R/3.0.1(default)
abokia-blast/2.0.2-130524/ompi_intel
abokia-blast/2.0.2-130630/ompi_intel
--------------------------- /soft/intel/modulefiles ----------------------------
advisor/2013/update1 intel/11.1.075 mkl/10.2.1.017
advisor/2013/update2 intel/11.1.080 mkl/10.2.5.035
advisor/2013/update3 intel/12.0 mkl/10.2.7.041
''')
resolver = ModuleDependencyResolver(None, modulecmd=module_script)
module = resolver.resolve(name="R", version=None, type="package")
assert module.module_name == "R"
assert module.module_version is None
module = resolver.resolve(name="R", version="3.0.1", type="package")
assert module.module_name == "R"
assert module.module_version == "3.0.1"
module = resolver.resolve(name="R", version="3.0.4", type="package")
assert module == INDETERMINATE_DEPENDENCY
def test_module_dependency_resolver():
with __test_base_path() as temp_directory:
module_script = os.path.join(temp_directory, "modulecmd")
__write_script(module_script, '''#!/bin/sh
cat %s/example_output 1>&2;
''' % temp_directory)
with open(os.path.join(temp_directory, "example_output"), "w") as f:
# Subset of module avail from MSI cluster.
f.write('''
-------------------------- /soft/modules/modulefiles ---------------------------
JAGS/3.2.0-gcc45
JAGS/3.3.0-gcc4.7.2
ProbABEL/0.1-3
ProbABEL/0.1-9e
R/2.12.2
R/2.13.1
R/2.14.1
R/2.15.0
R/2.15.1
R/3.0.1(default)
abokia-blast/2.0.2-130524/ompi_intel
abokia-blast/2.0.2-130630/ompi_intel
--------------------------- /soft/intel/modulefiles ----------------------------
advisor/2013/update1 intel/11.1.075 mkl/10.2.1.017
advisor/2013/update2 intel/11.1.080 mkl/10.2.5.035
advisor/2013/update3 intel/12.0 mkl/10.2.7.041
''')
resolver = ModuleDependencyResolver(None, modulecmd=module_script)
module = resolver.resolve( name="R", version=None, type="package" )
assert module.module_name == "R"
assert module.module_version == None
module = resolver.resolve( name="R", version="3.0.1", type="package" )
assert module.module_name == "R"
assert module.module_version == "3.0.1"
module = resolver.resolve( name="R", version="3.0.4", type="package" )
assert module == INDETERMINATE_DEPENDENCY
def test_module_resolver_with_mapping_versions():
with __test_base_path() as temp_directory:
module_script = _setup_module_command(temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
blast/2.22.0-mpi
blast/2.23
blast/2.24.0-mpi
''')
mapping_file = os.path.join(temp_directory, "mapping")
with open(mapping_file, "w") as f:
f.write('''
- from:
name: blast+
version: 2.24
to:
name: blast
version: 2.24.0-mpi
- from:
name: blast
version: 2.22
to:
version: 2.22.0-mpi
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
module = resolver.resolve(ToolRequirement(name="blast+", version="2.24", type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.24.0-mpi", module.module_version
resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
module = resolver.resolve(ToolRequirement(name="blast+", version="2.23", type="package"))
assert isinstance(module, NullDependency)
module = resolver.resolve(ToolRequirement(name="blast", version="2.22", type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.22.0-mpi", module.module_version
def test_module_resolver_with_mapping():
with __test_base_path() as temp_directory:
module_script = _setup_module_command(temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
blast/2.24
''')
mapping_file = os.path.join(temp_directory, "mapping")
with open(mapping_file, "w") as f:
f.write('''
- from: blast+
to: blast
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
module = resolver.resolve(ToolRequirement(name="blast+", version="2.24", type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.24", module.module_version
def test_module_resolver_with_mapping():
with __test_base_path() as temp_directory:
module_script = _setup_module_command(temp_directory, '''
-------------------------- /soft/modules/modulefiles ---------------------------
blast/2.24
''')
mapping_file = os.path.join(temp_directory, "mapping")
with open(mapping_file, "w") as f:
f.write('''
- from: blast+
to: blast
''')
resolver = ModuleDependencyResolver(_SimpleDependencyManager(), modulecmd=module_script, mapping_files=mapping_file)
module = resolver.resolve(ToolRequirement(name="blast+", version="2.24", type="package"))
assert module.module_name == "blast"
assert module.module_version == "2.24", module.module_version