def __init__(self, *args, **kwargs):
self.command_log, self.message_log = [], []
DXExecDependencyInstaller.__init__(self, *args, **kwargs)
def __init__(self, *args, **kwargs):
self.command_log, self.message_log = [], []
DXExecDependencyInstaller.__init__(self, *args, **kwargs)
def test_dx_execdepends_installer(self):
def get_edi(run_spec, job_desc=None):
return TestEDI(executable_desc={"runSpec": run_spec},
job_desc=job_desc if job_desc else {})
def assert_cmd_ran(edi, regexp):
self.assertRegexpMatches("\n".join(edi.command_log), regexp)
def assert_log_contains(edi, regexp):
self.assertRegexpMatches("\n".join(edi.message_log), regexp)
with self.assertRaisesRegexp(AppInternalError,
'Expected field "runSpec" to be present'):
DXExecDependencyInstaller({}, {})
with self.assertRaisesRegexp(AppInternalError,
'Expected field "name" to be present'):
get_edi({"dependencies": [{"foo": "bar"}]})
edi = get_edi({
"dependencies": [{
"name": "foo",
"package_manager": "cran",
"version": "1.2.3"
}]
})
edi.install()
assert_cmd_ran(
edi,
"R -e .+ install.packages.+devtools.+install_version.+foo.+version.+1.2.3"
)
with self.assertRaisesRegexp(AppInternalError,
'does not have a "url" field'):
get_edi(
{"dependencies": [{
"name": "foo",
"package_manager": "git"
}]})
edi = get_edi({
"execDepends": [{
"name": "git"
}],
"dependencies": [{
"name": "tmux"
}]
})
edi.install()
assert_cmd_ran(
edi, "apt-get install --yes --no-install-recommends git tmux")
edi = get_edi({})
edi.install()
edi = get_edi({
"execDepends": [],
"bundledDepends": [],
"dependencies": []
})
edi.install()
edi = get_edi({
"dependencies": [{
"name": "pytz",
"package_manager": "pip",
"version": "2014.7"
}, {
"name": "certifi",
"package_manager": "pip",
"stages": ["main"]
}, {
"name": "tmux",
"package_manager": "apt"
}, {
"name": "rake",
"package_manager": "gem",
"version": "10.3.2"
}, {
"name": "nokogiri",
"package_manager": "gem",
"stages": ["main"]
}, {
"name": "Module::Provision",
"package_manager": "cpan",
"version": "0.36.1"
}, {
"name": "LWP::MediaTypes",
"package_manager": "cpan"
}, {
"name": "RJSONIO",
"package_manager": "cran"
}, {
"name": "plyr",
"package_manager": "cran",
"version": "1.8.1"
}, {
"name": "ggplot2",
"package_manager": "cran",
"stages": ["main"],
"version": "1.0.1"
}, {
"name": "r1",
"id": {
"$dnanexus_link": "record-123"
}
}, {
"name": "g1",
"package_manager": "git",
"url": "https://github.com/dnanexus/oauth2-demo"
}, {
"name": "g2",
"package_manager": "git",
"url": "https://github.com/dnanexus/bwa",
"tag": "production",
"destdir": "/tmp/ee-edi-test-bwa",
"buld_commands": "echo build bwa here",
"stages": ["main"]
}]
})
edi.install()
assert_cmd_ran(edi,
re.escape("pip install --upgrade pytz==2014.7 certifi"))
assert_cmd_ran(edi,
"apt-get install --yes --no-install-recommends tmux")
assert_cmd_ran(
edi,
re.escape(
"gem install rake --version 10.3.2 && gem install nokogiri"))
assert_cmd_ran(
edi,
"R -e .+ install.packages.+\"RJSONIO\".+install_version.+\"ggplot2\".+version=\"1.0.1\""
)
assert_log_contains(
edi,
'Skipping bundled dependency "r1" because it does not refer to a file'
)
assert_cmd_ran(
edi,
re.escape(
"cd $(mktemp -d) && git clone https://github.com/dnanexus/oauth2-demo"
))
assert_cmd_ran(
edi,
"cd /tmp/ee-edi-test-bwa && git clone https://github.com/dnanexus/bwa"
)
assert_cmd_ran(edi, "git checkout production")
edi = get_edi({
"execDepends": [{
"name": "w00t",
"stages": ["foo", "bar"]
}, {
"name": "f1",
"id": {
"$dnanexus_link": "file-123"
},
"stages": ["xyzzt"]
}]
})
edi.install()
self.assertNotRegexpMatches("\n".join(edi.command_log), "w00t")
for name in "w00t", "f1":
assert_log_contains(
edi,
"Skipping dependency {} because it is inactive in stage \(function\) main"
.format(name))
edi = get_edi(
{"execDepends": [{
"name": "git",
"stages": ["foo", "bar"]
}]},
job_desc={"function": "foo"})
edi.install()
assert_cmd_ran(edi,
"apt-get install --yes --no-install-recommends git")
def install_run_spec(exec_depends):
run_spec = {"runSpec": {"execDepends": exec_depends}}
job_desc = dxpy.get_handler(dxpy.JOB_ID).describe()
dx_installer = DXExecDependencyInstaller(run_spec, job_desc)
dx_installer.install()
