def test_get_appet_with_asset(self):
bundle_name = "test-bundle-depends.tar.gz"
bundle_tmp_dir = tempfile.mkdtemp()
os.mkdir(os.path.join(bundle_tmp_dir, "a"))
with open(os.path.join(bundle_tmp_dir, 'a', 'foo.txt'), 'w') as file_in_bundle:
file_in_bundle.write('foo\n')
subprocess.check_call(['tar', '-czf', os.path.join(bundle_tmp_dir, bundle_name),
'-C', os.path.join(bundle_tmp_dir, 'a'), '.'])
bundle_file = dxpy.upload_local_file(filename=os.path.join(bundle_tmp_dir, bundle_name),
project=self.project,
wait_on_close=True)
asset_file = dxpy.upload_local_file(filename=os.path.join(bundle_tmp_dir, bundle_name),
project=self.project,
wait_on_close=True)
dxrecord_details = {"archiveFileId": {"$dnanexus_link": asset_file.get_id()}}
dxrecord = dxpy.new_dxrecord(project=self.project, types=["AssetBundle"], details=dxrecord_details,
name='asset-lib-test', properties={"version": "0.0.1"})
dxrecord.close()
asset_bundle_id = dxrecord.get_id()
asset_file.set_properties({"AssetBundle": asset_bundle_id})
code_str = """#!/bin/bash
main(){
echo 'Hello World'
}
"""
app_spec = {
"name": "asset_depends",
"dxapi": "1.0.0",
"runSpec": {
"code": code_str,
"interpreter": "bash",
"assetDepends": [{"id": asset_bundle_id}],
"bundledDepends": [{"name": bundle_name, "id": {"$dnanexus_link": bundle_file.get_id()}}]
},
"inputSpec": [],
"outputSpec": [],
"version": "1.0.0"
}
app_dir = self.write_app_directory("asset_depends", json.dumps(app_spec))
asset_applet_id = json.loads(run("dx build --json {app_dir}".format(app_dir=app_dir)))["id"]
with chdir(tempfile.mkdtemp()):
run("dx get --omit-resources " + asset_applet_id)
self.assertTrue(os.path.exists("asset_depends"))
self.assertFalse(os.path.exists(os.path.join("asset_depends", "resources")))
self.assertTrue(os.path.exists(os.path.join("asset_depends", "dxapp.json")))
applet_spec = json.load(open(os.path.join("asset_depends", "dxapp.json")))
self.assertEqual([{"name": "asset-lib-test",
"project": self.project,
"folder": "/",
"version": "0.0.1"}
],
applet_spec["runSpec"]["assetDepends"])
self.assertEqual([{"name": bundle_name, "id": {"$dnanexus_link": bundle_file.get_id()}}],
applet_spec["runSpec"]["bundledDepends"])
def test_file_name_with_special_chars_locally(self):
# create a tar.gz file with spaces, quotes and escape chars in its name
bundle_name = "test 'bundle' \"with\" \"@#^&%()[]{}\" spaces.tar.gz"
bundle_tmp_dir = tempfile.mkdtemp()
os.mkdir(os.path.join(bundle_tmp_dir, "a"))
with open(os.path.join(bundle_tmp_dir, 'a', 'foo.txt'), 'w') as file_in_bundle:
file_in_bundle.write('foo\n')
subprocess.check_call(['tar', '-czf', os.path.join(bundle_tmp_dir, bundle_name),
'-C', os.path.join(bundle_tmp_dir, 'a'), '.'])
extract_tmp_dir = tempfile.mkdtemp()
with chdir(extract_tmp_dir):
subprocess.check_call(["dx-unpack", os.path.join(bundle_tmp_dir, bundle_name)])
self.assertTrue(os.path.exists(os.path.join(extract_tmp_dir, 'foo.txt')))
def test_remove_file_after_unpack(self):
# dx-unpack removes the file after unpacking
bundle_name = "tarball.tar.gz"
bundle_tmp_dir = tempfile.mkdtemp()
os.mkdir(os.path.join(bundle_tmp_dir, "a"))
with open(os.path.join(bundle_tmp_dir, 'a', 'foo.txt'), 'w') as file_in_bundle:
file_in_bundle.write('foo\n')
subprocess.check_call(['tar', '-czf', os.path.join(bundle_tmp_dir, bundle_name),
'-C', os.path.join(bundle_tmp_dir, 'a'), '.'])
extract_tmp_dir = tempfile.mkdtemp()
with chdir(extract_tmp_dir):
subprocess.check_call(["dx-unpack", os.path.join(bundle_tmp_dir, bundle_name)])
self.assertTrue(os.path.exists(os.path.join(extract_tmp_dir, 'foo.txt')))
shutil.rmtree(os.path.join(bundle_tmp_dir, "a"))
self.assertFalse(os.path.exists(os.path.join(bundle_tmp_dir, bundle_name)))
def test_file_name_with_special_chars_locally(self):
# create a tar.gz file with spaces, quotes and escape chars in its name
bundle_name = "test 'bundle' \"with\" \"@#^&%()[]{}\" spaces.tar.gz"
bundle_tmp_dir = tempfile.mkdtemp()
os.mkdir(os.path.join(bundle_tmp_dir, "a"))
with open(os.path.join(bundle_tmp_dir, 'a', 'foo.txt'),
'w') as file_in_bundle:
file_in_bundle.write('foo\n')
subprocess.check_call([
'tar', '-czf',
os.path.join(bundle_tmp_dir, bundle_name), '-C',
os.path.join(bundle_tmp_dir, 'a'), '.'
])
extract_tmp_dir = tempfile.mkdtemp()
with chdir(extract_tmp_dir):
subprocess.check_call(
["dx-unpack",
os.path.join(bundle_tmp_dir, bundle_name)])
self.assertTrue(
os.path.exists(os.path.join(extract_tmp_dir, 'foo.txt')))
def test_remove_file_after_unpack(self):
# dx-unpack removes the file after unpacking
bundle_name = "tarball.tar.gz"
bundle_tmp_dir = tempfile.mkdtemp()
os.mkdir(os.path.join(bundle_tmp_dir, "a"))
with open(os.path.join(bundle_tmp_dir, 'a', 'foo.txt'),
'w') as file_in_bundle:
file_in_bundle.write('foo\n')
subprocess.check_call([
'tar', '-czf',
os.path.join(bundle_tmp_dir, bundle_name), '-C',
os.path.join(bundle_tmp_dir, 'a'), '.'
])
extract_tmp_dir = tempfile.mkdtemp()
with chdir(extract_tmp_dir):
subprocess.check_call(
["dx-unpack",
os.path.join(bundle_tmp_dir, bundle_name)])
self.assertTrue(
os.path.exists(os.path.join(extract_tmp_dir, 'foo.txt')))
shutil.rmtree(os.path.join(bundle_tmp_dir, "a"))
self.assertFalse(
os.path.exists(os.path.join(bundle_tmp_dir, bundle_name)))
def test_get_appet_with_asset(self):
bundle_name = "test-bundle-depends.tar.gz"
bundle_tmp_dir = tempfile.mkdtemp()
os.mkdir(os.path.join(bundle_tmp_dir, "a"))
with open(os.path.join(bundle_tmp_dir, 'a', 'foo.txt'),
'w') as file_in_bundle:
file_in_bundle.write('foo\n')
subprocess.check_call([
'tar', '-czf',
os.path.join(bundle_tmp_dir, bundle_name), '-C',
os.path.join(bundle_tmp_dir, 'a'), '.'
])
bundle_file = dxpy.upload_local_file(filename=os.path.join(
bundle_tmp_dir, bundle_name),
project=self.project,
wait_on_close=True)
asset_file = dxpy.upload_local_file(filename=os.path.join(
bundle_tmp_dir, bundle_name),
project=self.project,
wait_on_close=True)
dxrecord_details = {
"archiveFileId": {
"$dnanexus_link": asset_file.get_id()
}
}
dxrecord = dxpy.new_dxrecord(project=self.project,
types=["AssetBundle"],
details=dxrecord_details,
name='asset-lib-test',
properties={"version": "0.0.1"})
dxrecord.close()
asset_bundle_id = dxrecord.get_id()
asset_file.set_properties({"AssetBundle": asset_bundle_id})
code_str = """#!/bin/bash
main(){
echo 'Hello World'
}
"""
app_spec = {
"name": "asset_depends",
"dxapi": "1.0.0",
"runSpec": {
"code":
code_str,
"interpreter":
"bash",
"distribution":
"Ubuntu",
"release":
"14.04",
"assetDepends": [{
"id": asset_bundle_id
}],
"bundledDepends": [{
"name": bundle_name,
"id": {
"$dnanexus_link": bundle_file.get_id()
}
}]
},
"inputSpec": [],
"outputSpec": [],
"version": "1.0.0"
}
app_dir = self.write_app_directory("asset_depends",
json.dumps(app_spec))
asset_applet_id = json.loads(
run("dx build --json {app_dir}".format(app_dir=app_dir)))["id"]
with chdir(tempfile.mkdtemp()):
run("dx get --omit-resources " + asset_applet_id)
self.assertTrue(os.path.exists("asset_depends"))
self.assertFalse(
os.path.exists(os.path.join("asset_depends", "resources")))
self.assertTrue(
os.path.exists(os.path.join("asset_depends", "dxapp.json")))
with open(os.path.join("asset_depends", "dxapp.json")) as fh:
applet_spec = json.load(fh)
self.assertEqual([{
"name": "asset-lib-test",
"project": self.project,
"folder": "/",
"version": "0.0.1"
}], applet_spec["runSpec"]["assetDepends"])
self.assertEqual([{
"name": bundle_name,
"id": {
"$dnanexus_link": bundle_file.get_id()
}
}], applet_spec["runSpec"]["bundledDepends"])
def setUp(self):
self.wd = tempfile.mkdtemp()
chdir(self.wd)
setUpTempProject(self)