def get_secret_templates(self):
def _secret(secret_name, secret):
template = CommentedMap()
template['force'] = secret.get('force', False)
template['apiVersion'] = 'v1'
template = CommentedMap()
template['apiVersion'] = self.DEFAULT_API_VERSION
template['kind'] = "Secret"
template['metadata'] = CommentedMap([('name', secret_name),
('namespace',
self._namespace_name)])
template['type'] = 'Opaque'
template['data'] = {}
for key, vault_variable in iteritems(secret):
template['data'][key] = "{{ %s | b64encode }}" % vault_variable
return template
templates = CommentedSeq()
if self._secrets:
for secret_name, secret_config in iteritems(self._secrets):
secret = _secret(secret_name, secret_config)
templates.append(secret)
return templates
def get_pvc_tasks(self, tags=[]):
module_name='k8s_v1_persistent_volume_claim'
tasks = CommentedSeq()
for template in self.get_pvc_templates():
task = CommentedMap()
task['name'] = 'Create PVC'
task[module_name] = CommentedMap()
task[module_name]['state'] = 'present'
if self._auth:
for key in self._auth:
task[module_name][key] = self._auth[key]
task[module_name]['force'] = template.pop('force', False)
task[module_name]['resource_definition'] = template
if tags:
task['tags'] = copy.copy(tags)
tasks.append(task)
if self._volumes:
# Remove any volumes where state is 'absent'
for volname, vol_config in self._volumes.items():
if self.CONFIG_KEY in vol_config:
if vol_config[self.CONFIG_KEY].get('state', 'present') == 'absent':
task = CommentedMap()
task['name'] = 'Remove PVC'
task[module_name] = CommentedMap()
task[module_name]['name'] = volname
task[module_name]['namespace'] = self._namespace_name
task[module_name]['state'] = 'absent'
if self._auth:
for key in self._auth:
task[module_name][key] = self._auth[key]
if tags:
task['tags'] = copy.copy(tags)
tasks.append(task)
return tasks
def get_deployment_tasks(self, module_name=None, engine_state=None, tags=[]):
tasks = CommentedSeq()
for template in self.get_deployment_templates(engine_state=engine_state):
task = CommentedMap()
if engine_state is None:
task_name = 'Create deployment, and scale replicas up'
else:
task_name = 'Stop running containers by scaling replicas down to 0'
task['name'] = task_name
task[module_name] = CommentedMap()
task[module_name]['state'] = 'present'
if self._auth:
for key in self._auth:
task[module_name][key] = self._auth[key]
task[module_name]['force'] = template.pop('force', False)
task[module_name]['resource_definition'] = template
if tags:
task['tags'] = copy.copy(tags)
tasks.append(task)
if engine_state != 'stop':
for name, service_config in self._services.items():
# Remove deployment for any services where state is 'absent'
if service_config.get(self.CONFIG_KEY, {}).get('state', 'present') == 'absent':
task['name'] = 'Remove deployment'
task[module_name] = CommentedMap()
task[module_name]['state'] = 'absent'
if self._auth:
for key in self._auth:
task[module_name][key] = self._auth[key]
task[module_name]['name'] = name
task[module_name]['namespace'] = self._namespace_name
if tags:
task['tags'] = copy.copy(tags)
tasks.append(task)
return tasks
def get_secret_templates(self):
def _secret(secret_name, secret):
template = CommentedMap()
template['force'] = secret.get('force', False)
template['apiVersion'] = 'v1'
template = CommentedMap()
template['apiVersion'] = self.DEFAULT_API_VERSION
template['kind'] = "Secret"
template['metadata'] = CommentedMap([
('name', secret_name),
('namespace', self._namespace_name)
])
template['type'] = 'Opaque'
template['data'] = {}
for key, vault_variable in iteritems(secret):
template['data'][key] = "{{ %s | b64encode }}" % vault_variable
return template
templates = CommentedSeq()
if self._secrets:
for secret_name, secret_config in iteritems(self._secrets):
secret = _secret(secret_name, secret_config)
templates.append(secret)
return templates
def get_service_tasks(self, tags=[]):
module_name='k8s_v1_service'
tasks = CommentedSeq()
for template in self.get_services_templates():
task = CommentedMap()
task['name'] = 'Create service'
task[module_name] = CommentedMap()
task[module_name]['state'] = 'present'
if self._auth:
for key in self._auth:
task[module_name][key] = self._auth[key]
task[module_name]['force'] = template.pop('force', False)
task[module_name]['resource_definition'] = template
if tags:
task['tags'] = copy.copy(tags)
tasks.append(task)
if self._services:
# Remove an services where state is 'absent'
for name, service in self._services.items():
if service.get(self.CONFIG_KEY, {}).get('state', 'present') == 'absent':
task = CommentedMap()
task['name'] = 'Remove service'
task[module_name] = CommentedMap()
task[module_name]['state'] = 'absent'
task[module_name]['name'] = name
task[module_name]['namespace'] = self._namespace_name
if self._auth:
for key in self._auth:
task[module_name][key] = self._auth[key]
if tags:
task['tags'] = copy.copy(tags)
tasks.append(task)
return tasks
def _merge_simple_lists(self, lhs: CommentedSeq, rhs: CommentedSeq,
path: YAMLPath,
node_coord: NodeCoords) -> CommentedSeq:
"""
Merge two CommentedSeq-wrapped lists of Scalars or CommentedSeqs.
Parameters:
1. lhs (CommentedSeq) The merge target.
2. rhs (CommentedSeq) The merge source.
3. path (YAMLPath) Location within the DOM where this merge is taking
place.
4. node_coord (NodeCoords) The RHS root node, its parent, and reference
within its parent; used for config lookups.
Returns: (list) The merged result.
Raises:
- `MergeException` when a clean merge is impossible.
"""
if not isinstance(lhs, CommentedSeq):
raise MergeException(
"Impossible to add Array data to non-Array destination.", path)
merge_mode = self.config.array_merge_mode(node_coord)
if merge_mode is ArrayMergeOpts.LEFT:
return lhs
if merge_mode is ArrayMergeOpts.RIGHT:
return rhs
tagless_lhs = Nodes.tagless_elements(lhs)
for idx, ele in enumerate(rhs):
path_next = path + "[{}]".format(idx)
self.logger.debug("Processing element {} at {}.".format(
idx, path_next),
prefix="Merger::_merge_simple_lists: ",
data=ele)
if merge_mode is ArrayMergeOpts.UNIQUE:
cmp_val = ele
if isinstance(ele, TaggedScalar):
cmp_val = ele.value
self.logger.debug(
"Looking for comparison value, {}, in:".format(cmp_val),
prefix="Merger::_merge_simple_lists: ",
data=tagless_lhs)
if cmp_val in tagless_lhs:
lhs = CommentedSeq([
ele if
(e == cmp_val or
(isinstance(e, TaggedScalar) and e.value == cmp_val))
else e for e in lhs
])
else:
lhs.append(ele)
continue
lhs.append(ele)
return lhs
def cli(sections, input, output, quiet):
# Set YAML parameters
yaml = YAML(typ="rt") # Round-trip mode allows for comment insertion
indent_offset = 2
yaml.indent(offset=indent_offset)
# Load environment file template
with open(os.path.join("requirements", "environment.in")) as f:
env_yml = yaml.load(f.read())
# Extract dependency section contents
if not quiet:
print(f"Reading dependencies from {input}")
setup_config = read_configuration(input)
sections = [x.strip() for x in sections.split(",")]
section_indices = dict()
dep_list = (deepcopy(env_yml["dependencies"])
if "dependencies" in env_yml else [])
i = len(dep_list)
for section in sections:
section_indices[section] = i
try:
packages = (setup_config["options"]["install_requires"]
if section == "main" else
setup_config["options"]["extras_require"][section])
except KeyError:
raise RuntimeError(f"Cannot fetch dependencies from {input}")
for package in packages:
if package not in dep_list: # Do not duplicate
dep_list.append(package)
i += 1
# Format dependency list
lst = CS(dep_list)
for section, i in section_indices.items():
lst.yaml_set_comment_before_after_key(i, section, indent_offset)
env_yml["dependencies"] = lst
# Output to terminal
if not quiet:
yaml.dump(env_yml, sys.stdout)
# Output to file
if output is not None:
with open(output, "w") as outfile:
if not quiet:
print()
print(f"Saving to {output}")
yaml.dump(env_yml, outfile)
def get_services_templates(self):
""" Generate a service configuration """
def _create_service(name, service):
template = CommentedMap()
state = service.get(self.CONFIG_KEY, {}).get('state', 'present')
if state == 'present':
ports = self.get_service_ports(service)
if ports:
template['apiVersion'] = self.DEFAULT_API_VERSION
template['kind'] = 'Service'
template['force'] = service.get(self.CONFIG_KEY, {}).get('service', {}).get('force', False)
labels = CommentedMap([
('app', self._namespace_name),
('service', name)
])
template['metadata'] = CommentedMap([
('name', name),
('namespace', self._namespace_name),
('labels', copy.deepcopy(labels))
])
template['spec'] = CommentedMap([
('selector', copy.deepcopy(labels)),
('ports', ports)
])
# Translate options:
if service.get(self.CONFIG_KEY):
for key, value in service[self.CONFIG_KEY].items():
if key == 'service':
for service_key, service_value in value.items():
if service_key == 'force':
continue
elif service_key == 'metadata':
self.copy_attribute(template, service_key, service_value)
else:
self.copy_attribute(template['spec'], service_key, service_value)
return template
templates = CommentedSeq()
if self._services:
for name, service in self._services.items():
template = _create_service(name, service)
if template:
templates.append(template)
if service.get('links'):
# create services for aliased links
for link in service['links']:
if ':' in link:
service_name, alias = link.split(':')
alias_config = self._services.get(service_name)
if alias_config:
new_service = _create_service(alias, alias_config)
if new_service:
templates.append(new_service)
return templates
def cmap(
d,
lc=None,
fn=None
): # type: (Union[int, float, str, Text, Dict, List], List[int], Text) -> Union[int, float, str, Text, CommentedMap, CommentedSeq]
if lc is None:
lc = [0, 0, 0, 0]
if fn is None:
fn = "test"
if isinstance(d, CommentedMap):
fn = d.lc.filename if hasattr(d.lc, "filename") else fn
for k, v in six.iteritems(d):
if k in d.lc.data:
d[k] = cmap(v, lc=d.lc.data[k], fn=fn)
else:
d[k] = cmap(v, lc, fn=fn)
return d
if isinstance(d, CommentedSeq):
fn = d.lc.filename if hasattr(d.lc, "filename") else fn
for k, v in enumerate(d):
if k in d.lc.data:
d[k] = cmap(v, lc=d.lc.data[k], fn=fn)
else:
d[k] = cmap(v, lc, fn=fn)
return d
if isinstance(d, dict):
cm = CommentedMap()
for k in sorted(d.keys()):
v = d[k]
if isinstance(v, CommentedBase):
uselc = [v.lc.line, v.lc.col, v.lc.line, v.lc.col]
vfn = v.lc.filename if hasattr(v.lc, "filename") else fn
else:
uselc = lc
vfn = fn
cm[k] = cmap(v, lc=uselc, fn=vfn)
cm.lc.add_kv_line_col(k, uselc)
cm.lc.filename = fn
return cm
if isinstance(d, list):
cs = CommentedSeq()
for k, v in enumerate(d):
if isinstance(v, CommentedBase):
uselc = [v.lc.line, v.lc.col, v.lc.line, v.lc.col]
vfn = v.lc.filename if hasattr(v.lc, "filename") else fn
else:
uselc = lc
vfn = fn
cs.append(cmap(v, lc=uselc, fn=vfn))
cs.lc.add_kv_line_col(k, uselc)
cs.lc.filename = fn
return cs
else:
return d
def cmap(
d, # type: Union[int, float, str, Text, Dict[Text, Any], List[Dict[Text, Any]]]
lc=None, # type: Optional[List[int]]
fn=None, # type: Optional[Text]
): # type: (...) -> Union[int, float, str, Text, CommentedMap, CommentedSeq]
if lc is None:
lc = [0, 0, 0, 0]
if fn is None:
fn = "test"
if isinstance(d, CommentedMap):
fn = d.lc.filename if hasattr(d.lc, "filename") else fn
for k, v in six.iteritems(d):
if d.lc.data is not None and k in d.lc.data:
d[k] = cmap(v, lc=d.lc.data[k], fn=fn)
else:
d[k] = cmap(v, lc, fn=fn)
return d
if isinstance(d, CommentedSeq):
fn = d.lc.filename if hasattr(d.lc, "filename") else fn
for k2, v2 in enumerate(d):
if d.lc.data is not None and k2 in d.lc.data:
d[k2] = cmap(v2, lc=d.lc.data[k2], fn=fn)
else:
d[k2] = cmap(v2, lc, fn=fn)
return d
if isinstance(d, MutableMapping):
cm = CommentedMap()
for k in sorted(d.keys()):
v = d[k]
if isinstance(v, CommentedBase):
uselc = [v.lc.line, v.lc.col, v.lc.line, v.lc.col]
vfn = v.lc.filename if hasattr(v.lc, "filename") else fn
else:
uselc = lc
vfn = fn
cm[k] = cmap(v, lc=uselc, fn=vfn)
cm.lc.add_kv_line_col(k, uselc)
cm.lc.filename = fn
return cm
if isinstance(d, MutableSequence):
cs = CommentedSeq()
for k3, v3 in enumerate(d):
if isinstance(v3, CommentedBase):
uselc = [v3.lc.line, v3.lc.col, v3.lc.line, v3.lc.col]
vfn = v3.lc.filename if hasattr(v3.lc, "filename") else fn
else:
uselc = lc
vfn = fn
cs.append(cmap(v3, lc=uselc, fn=vfn))
cs.lc.add_kv_line_col(k3, uselc)
cs.lc.filename = fn
return cs
else:
return d
def update_environment_yml():
"""Update conda_dev_env.yml file for conda."""
import re
from ruamel.yaml import YAML
from ruamel.yaml.comments import CommentedMap, CommentedSeq
environment_filename = "conda_dev_env.yml"
cmap = CommentedMap()
cmap.yaml_set_start_comment(
("Usage: conda env create -n myenvname -f {} python=3.6\n"
" conda activate myenvname\n"
" pip install --no-deps -e .".format(environment_filename)))
cmap["name"] = "aiida_crystal17"
cmap["channels"] = CommentedSeq(["conda-forge", "cjs14"])
cmap["channels"].yaml_add_eol_comment("for sqlalchemy-diff and pgtest", 1)
cmap["dependencies"] = dmap = CommentedSeq()
# additional packages
dmap.append("pip")
dmap.append("aiida-core.services")
# fix incompatibilities between conda and pypi
replacements = {"pre-commit": "pre_commit"}
setup_json = get_setup_json()
for base, key in [
(None, "install_requires"),
("extras_require", "testing"),
("extras_require", "code_style"),
("extras_require", "docs"),
]:
requirements = setup_json.get(base, setup_json)[key]
count = 0
for req in sorted(requirements, key=lambda x: x.lower()):
# skip packages required for specific python versions < 3
if re.findall("python_version\\s*\\<\\s*\\'?3", req):
continue
req = req.split(";")[0]
for (regex, replacement) in iter(replacements.items()):
req = re.sub(regex, replacement, req)
count += 1
dmap.append(req.lower())
dmap.yaml_set_comment_before_after_key(len(dmap) - count, before=key)
yaml = YAML(typ="rt")
yaml.default_flow_style = False
yaml.encoding = "utf-8"
yaml.allow_unicode = True
file_path = os.path.join(ROOT_DIR, environment_filename)
with open(file_path, "w") as env_file:
yaml.dump(cmap, env_file)
def __delitem__(self, i):
if isinstance(i, str):
r = [ii for ii, x in enumerate(self) if x.get('name', None) == i]
if len(r) > 1:
raise KeyError(
"There are {} elements named {}.".format(len(r), i))
elif len(r) == 0:
raise KeyError("No element named {} found.".format(i))
else:
CommentedSeq.__delitem__(self, r[0])
else:
return CommentedSeq.__delitem__(self, i)
def __setitem__(self, i, v):
if isinstance(i, str):
r = [(ii, x) for ii, x in enumerate(self)
if x.get('name', None) == i]
if len(r) > 1:
raise KeyError("There are {} elements named {}.".format(
len(r), i))
elif len(r) == 0:
self.append(v)
else:
CommentedSeq.__setitem__(self, r[0][0], v)
else:
CommentedSeq.__setitem__(self, i, v)
def split_container_config(input_data):
components = sort_components_based_on_execution_id(input_data)
updated_components = CommentedSeq()
for component in components:
container_count = component['deploy']['container_count']
for i in range(0, container_count):
temp_component = copy.deepcopy(component)
temp_component['container_count'] = 1
temp_component['id'] = component['execution_id'] + 0
del temp_component['execution_id']
updated_components.append(temp_component)
input_data['lightweight_components'] = updated_components
return input_data
def cmap(d, lc=None, fn=None): # type: (Union[int, float, str, Text, Dict, List], List[int], Text) -> Union[int, float, str, Text, CommentedMap, CommentedSeq]
if lc is None:
lc = [0, 0, 0, 0]
if fn is None:
fn = "test"
if isinstance(d, CommentedMap):
fn = d.lc.filename if hasattr(d.lc, "filename") else fn
for k,v in six.iteritems(d):
if k in d.lc.data:
d[k] = cmap(v, lc=d.lc.data[k], fn=fn)
else:
d[k] = cmap(v, lc, fn=fn)
return d
if isinstance(d, CommentedSeq):
fn = d.lc.filename if hasattr(d.lc, "filename") else fn
for k,v in enumerate(d):
if k in d.lc.data:
d[k] = cmap(v, lc=d.lc.data[k], fn=fn)
else:
d[k] = cmap(v, lc, fn=fn)
return d
if isinstance(d, dict):
cm = CommentedMap()
for k in sorted(d.keys()):
v = d[k]
if isinstance(v, CommentedBase):
uselc = [v.lc.line, v.lc.col, v.lc.line, v.lc.col]
vfn = v.lc.filename if hasattr(v.lc, "filename") else fn
else:
uselc = lc
vfn = fn
cm[k] = cmap(v, lc=uselc, fn=vfn)
cm.lc.add_kv_line_col(k, uselc)
cm.lc.filename = fn
return cm
if isinstance(d, list):
cs = CommentedSeq()
for k,v in enumerate(d):
if isinstance(v, CommentedBase):
uselc = [v.lc.line, v.lc.col, v.lc.line, v.lc.col]
vfn = v.lc.filename if hasattr(v.lc, "filename") else fn
else:
uselc = lc
vfn = fn
cs.append(cmap(v, lc=uselc, fn=vfn))
cs.lc.add_kv_line_col(k, uselc)
cs.lc.filename = fn
return cs
else:
return d
def create_default_seq(config):
if not config.get('config'):
config['config'] = CommentedSeq()
if not config.get('package'):
config['package'] = CommentedSeq()
if not config.get('ignore'):
config['ignore'] = CommentedSeq()
if not isinstance(config['config'], list):
config['config'] = list_to_seq(config['config'])
if not isinstance(config['package'], list):
config['package'] = list_to_seq(config['package'])
if not isinstance(config['ignore'], list):
config['ignore'] = list_to_seq(config['ignore'])
return config
def _resolve_idmap(
self,
document: CommentedMap,
loader: "Loader",
) -> None:
# Convert fields with mapSubject into lists
# use mapPredicate if the mapped value isn't a dict.
for idmapField in loader.idmap:
if idmapField in document:
idmapFieldValue = document[idmapField]
if (
isinstance(idmapFieldValue, MutableMapping)
and "$import" not in idmapFieldValue
and "$include" not in idmapFieldValue
):
ls = CommentedSeq()
for k in sorted(idmapFieldValue.keys()):
val = idmapFieldValue[k]
v = None # type: Optional[CommentedMap]
if not isinstance(val, CommentedMap):
if idmapField in loader.mapPredicate:
v = CommentedMap(
((loader.mapPredicate[idmapField], val),)
)
v.lc.add_kv_line_col(
loader.mapPredicate[idmapField],
document[idmapField].lc.data[k],
)
v.lc.filename = document.lc.filename
else:
raise ValidationException(
"mapSubject '{}' value '{}' is not a dict "
"and does not have a mapPredicate.".format(k, v)
)
else:
v = val
v[loader.idmap[idmapField]] = k
v.lc.add_kv_line_col(
loader.idmap[idmapField], document[idmapField].lc.data[k]
)
v.lc.filename = document.lc.filename
ls.lc.add_kv_line_col(len(ls), document[idmapField].lc.data[k])
ls.lc.filename = document.lc.filename
ls.append(v)
document[idmapField] = ls
def generate_orchestration_playbook(self, url=None, namespace=None, local_images=True, **kwargs):
"""
Generate an Ansible playbook to orchestrate services.
:param url: registry URL where images will be pulled from
:param namespace: registry namespace
:param local_images: bypass pulling images, and use local copies
:return: playbook dict
"""
for service_name in self.services:
image = self.get_latest_image_for_service(service_name)
if local_images:
self.services[service_name]['image'] = image.tags[0]
else:
if namespace is not None:
image_url = urljoin('{}/'.format(urljoin(url, namespace)), image.tags[0])
else:
image_url = urljoin(url, image.tags[0])
self.services[service_name]['image'] = image_url
if kwargs.get('k8s_auth'):
self.k8s_client.set_authorization(kwargs['auth'])
play = CommentedMap()
play['name'] = u'Manage the lifecycle of {} on {}'.format(self.project_name, self.display_name)
play['hosts'] = 'localhost'
play['gather_facts'] = 'no'
play['connection'] = 'local'
play['roles'] = CommentedSeq()
play['tasks'] = CommentedSeq()
role = CommentedMap([
('role', 'kubernetes-modules')
])
play['roles'].append(role)
play.yaml_set_comment_before_after_key(
'roles', before='Include Ansible Kubernetes and OpenShift modules', indent=4)
play.yaml_set_comment_before_after_key('tasks', before='Tasks for setting the application state. '
'Valid tags include: start, stop, restart, destroy', indent=4)
play['tasks'].append(self.deploy.get_namespace_task(state='present', tags=['start']))
play['tasks'].append(self.deploy.get_namespace_task(state='absent', tags=['destroy']))
play['tasks'].extend(self.deploy.get_service_tasks(tags=['start']))
play['tasks'].extend(self.deploy.get_deployment_tasks(engine_state='stop', tags=['stop', 'restart']))
play['tasks'].extend(self.deploy.get_deployment_tasks(tags=['start', 'restart']))
play['tasks'].extend(self.deploy.get_pvc_tasks(tags=['start']))
playbook = CommentedSeq()
playbook.append(play)
logger.debug(u'Created playbook to run project', playbook=playbook)
return playbook
def split_component_config(input_data):
components = input_data['lightweight_components']
updated_components = CommentedSeq()
## deep copy
for component in components:
for idx, val in enumerate(component['deploy']):
temp_component = copy.deepcopy(component)
temp_component['deploy'] = copy.deepcopy(component['deploy'][idx])
#temp_component['execution_id'] = copy.deepcopy(component['execution_id'])
updated_components.append(temp_component)
components = updated_components
input_data['lightweight_components'] = components
return input_data
def test_recipe():
seq = CommentedSeq(["importlib-metadata >=0.12", "pytest"])
seq.yaml_add_eol_comment("[py<38]", 0)
item = RecipeItem(0, seq)
assert item.value == "importlib-metadata >=0.12"
assert item.selector == "py<38"
assert str(item) == "importlib-metadata >=0.12 # [py<38]"
item.value = "importlib-metadata"
item.selector = "py35"
assert item.value == "importlib-metadata"
assert item.selector == "py35"
assert seq.ca.items[0][0].value == " # [py35]"
assert seq[0] == "importlib-metadata"
assert str(item) == "importlib-metadata # [py35]"
def update_secondaryFiles(t, top=False):
# type: (Any, bool) -> Union[MutableSequence[MutableMapping[str, str]], MutableMapping[str, str]]
if isinstance(t, CommentedSeq):
new_seq = copy.deepcopy(t)
for index, entry in enumerate(t):
new_seq[index] = update_secondaryFiles(entry)
return new_seq
elif isinstance(t, MutableSequence):
return CommentedSeq([update_secondaryFiles(p) for p in t])
elif isinstance(t, MutableMapping):
return t
elif top:
return CommentedSeq([CommentedMap([("pattern", t)])])
else:
return CommentedMap([("pattern", t)])
def get_pvc_templates(self):
def _volume_to_pvc(claim_name, claim):
template = CommentedMap()
template['force'] = claim.get('force', False)
template['apiVersion'] = 'v1'
template = CommentedMap()
template['apiVersion'] = self.DEFAULT_API_VERSION
template['kind'] = "PersistentVolumeClaim"
template['metadata'] = CommentedMap([('name', claim_name),
('namespace',
self._namespace_name)])
template['spec'] = CommentedMap()
template['spec']['resources'] = {'requests': {'storage': '1Gi'}}
if claim.get('volume_name'):
template['spec']['volumeName'] = claim['volume_name']
if claim.get('access_modes'):
template['spec']['accessModes'] = claim['access_modes']
if claim.get('requested_storage'):
template['spec']['resources']['requests']['storage'] = claim[
'requested_storage']
if claim.get('storage_class'):
if not template['metadata'].get('annotations'):
template['metadata']['annotations'] = {}
template['metadata']['annotations']['storageClass'] = claim[
'storage_class'] #TODO verify this syntax
if claim.get('selector'):
if claim['selector'].get('match_labels'):
if not template['spec'].get('selector'):
template['spec']['selector'] = dict()
template['spec']['selector']['matchLabels'] = claim[
'match_labels']
if claim['selector'].get('match_expressions'):
if not template['spec'].get('selector'):
template['spec']['selector'] = dict()
template['spec']['selector']['matchExpressions'] = claim[
'match_expressions']
return template
templates = CommentedSeq()
if self._volumes:
for volname, vol_config in iteritems(self._volumes):
if self.CONFIG_KEY in vol_config:
if vol_config[self.CONFIG_KEY].get('state',
'present') == 'present':
volume = _volume_to_pvc(volname,
vol_config[self.CONFIG_KEY])
templates.append(volume)
return templates
def test_rdf_datetime() -> None:
"""Affirm that datetime objects can be serialized in makerdf()."""
ldr = Loader({})
ctx: ContextType = {
"id": "@id",
"location": {"@id": "@id", "@type": "@id"},
"bar": "http://example.com/bar",
"ex": "http://example.com/",
}
ldr.add_context(ctx)
ra: CommentedMap = cast(
CommentedMap,
ldr.resolve_all(
cmap(
{
"id": "foo",
"bar": {"id": "baz"},
}
),
"http://example.com",
)[0],
)
ra["s:dateCreated"] = datetime.datetime(2020, 10, 8)
g = makerdf(None, ra, ctx)
g.serialize(destination=stdout(), format="n3")
g2 = makerdf(None, CommentedSeq([ra]), ctx)
g2.serialize(destination=stdout(), format="n3")
def to_yaml(self, data):
self._should_be_list(data)
# TODO : Different length string
return CommentedSeq([
validator.to_yaml(item)
for item, validator in zip(data, self._validators)
])
def ruamel_structure(data, validator=None):
"""
Take dicts and lists and return a ruamel.yaml style
structure of CommentedMaps, CommentedSeqs and
data.
If a validator is presented and the type is unknown,
it is checked against the validator to see if it will
turn it back in to YAML.
"""
if isinstance(data, dict):
if len(data) == 0:
raise exceptions.CannotBuildDocumentsFromEmptyDictOrList(
"Document must be built with non-empty dicts and lists")
return CommentedMap([(ruamel_structure(key), ruamel_structure(value))
for key, value in data.items()])
elif isinstance(data, list):
if len(data) == 0:
raise exceptions.CannotBuildDocumentsFromEmptyDictOrList(
"Document must be built with non-empty dicts and lists")
return CommentedSeq([ruamel_structure(item) for item in data])
elif isinstance(data, bool):
return u"yes" if data else u"no"
elif isinstance(data, (int, float)):
return str(data)
else:
if not is_string(data):
raise exceptions.CannotBuildDocumentFromInvalidData(
("Document must be built from a combination of:\n"
"string, int, float, bool or nonempty list/dict\n\n"
"Instead, found variable with type '{}': '{}'").format(
type(data).__name__, data))
return data
def build_next_node(yaml_path: YAMLPath,
depth: int,
value: Any = None) -> Any:
"""
Get the best default value for the next entry in a YAML Path.
Parameters:
1. yaml_path (deque) The pre-parsed YAML Path to follow
2. depth (int) Index of the YAML Path segment to evaluate
3. value (Any) The expected value for the final YAML Path entry
Returns: (Any) The most appropriate default value
Raises: N/A
"""
default_value = Nodes.wrap_type(value)
segments = yaml_path.escaped
if not (segments and len(segments) > depth):
return default_value
typ = segments[depth][0]
if typ == PathSegmentTypes.INDEX:
default_value = CommentedSeq()
elif typ == PathSegmentTypes.KEY:
default_value = CommentedMap()
return default_value
def saveenroll():
"""Save and Enroll"""
global dir
try:
yaml = YAML()
with open(cmd + "/client-config.yaml") as fp:
data = yaml.load(fp)
data['url'] = "http://" + addr
data['mspdir'] = dir + "/msp"
data['csr']['cn'] = t5.get()
f = CommentedSeq([
CommentedMap([('C', t6.get()), ('ST', t7.get()),
('L', t8.get()), ('O', t9.get()),
('OU', t10.get())])
])
data['csr']['names'] = f
fp = open(cmd + "/client-config.yaml", "w")
yaml.dump(data, fp)
res = check_output(
"cd " + cmd + "; export FABRIC_CA_CLIENT_HOME=" + dir +
"; fabric-ca-client enroll -c client-config.yaml -u http://" +
t11.get() + ":" + t12.get() + "@" + addr,
shell=True)
except Exception as e:
error(str(e))
print(res)
tkMessageBox.showinfo(message="Successfully Enrolled")
def _migrate_decorators(self, element, old_key, new_key):
self.log.debug("Converting display_element blink decorator to widget "
"animation")
decorator = element[old_key]
element[new_key] = CommentedMap()
element[new_key]['show_slide'] = CommentedSeq()
on_dict = CommentedMap()
on_dict['property'] = 'opacity'
on_dict['value'] = 1
on_dict['duration'] = str(decorator.get('on_secs', .5)) + 's'
element[new_key]['show_slide'].append(on_dict)
off_dict = CommentedMap()
off_dict['property'] = 'opacity'
off_dict['value'] = 0
off_dict['duration'] = str(decorator.get('off_secs', .5)) + 's'
off_dict['repeat'] = True
element[new_key]['show_slide'].append(off_dict)
del element[old_key]
return element
def FSlist(l): # concert list into flow-style (default is block style)
from ruamel.yaml.comments import CommentedSeq
double_quoted_list = [DoubleQuotedScalarString(x) for x in l]
cs = CommentedSeq(double_quoted_list)
cs.fa.set_flow_style()
return cs
def _type_dsl(
self,
t: Union[str, CommentedMap, CommentedSeq],
lc: LineCol,
filename: str,
) -> Union[str, CommentedMap, CommentedSeq]:
if not isinstance(t, str):
return t
m = typeDSLregex.match(t)
if not m:
return t
first = m.group(1)
assert first
second = third = None
if bool(m.group(2)):
second = CommentedMap((("type", "array"), ("items", first)))
second.lc.add_kv_line_col("type", lc)
second.lc.add_kv_line_col("items", lc)
second.lc.filename = filename
if bool(m.group(3)):
third = CommentedSeq(["null", second or first])
third.lc.add_kv_line_col(0, lc)
third.lc.add_kv_line_col(1, lc)
third.lc.filename = filename
return third or second or first
def seq(self, *args):
# type: (Any) -> Any
if self.typ == 'rt':
from ruamel.yaml.comments import CommentedSeq
return CommentedSeq(*args)
else:
return list(*args)
def _type_dsl(
self,
t, # type: Union[Text, Dict, List]
lc,
filename):
# type: (...) -> Union[Text, Dict[Text, Text], List[Union[Text, Dict[Text, Text]]]]
if not isinstance(t, (str, six.text_type)):
return t
m = Loader.typeDSLregex.match(t)
if not m:
return t
first = m.group(1)
second = third = None
if bool(m.group(2)):
second = CommentedMap((("type", "array"), ("items", first)))
second.lc.add_kv_line_col("type", lc)
second.lc.add_kv_line_col("items", lc)
second.lc.filename = filename
if bool(m.group(3)):
third = CommentedSeq([u"null", second or first])
third.lc.add_kv_line_col(0, lc)
third.lc.add_kv_line_col(1, lc)
third.lc.filename = filename
return third or second or first
def wrap_type(value: Any) -> Any:
"""
Wrap a value in one of the ruamel.yaml wrapper types.
Parameters:
1. value (Any) The value to wrap.
Returns: (Any) The wrapped value or the original value when a better
wrapper could not be identified.
Raises: N/A
"""
wrapped_value = value
ast_value = Nodes.typed_value(value)
typ = type(ast_value)
if typ is list:
wrapped_value = CommentedSeq(value)
elif typ is dict:
wrapped_value = CommentedMap(value)
elif typ is str:
wrapped_value = PlainScalarString(value)
elif typ is int:
wrapped_value = ScalarInt(value)
elif typ is float:
wrapped_value = Nodes.make_float_node(ast_value)
elif typ is bool:
wrapped_value = ScalarBoolean(bool(value))
return wrapped_value
def update_environment_yml():
"""
Updates conda_dev_env.yml file for conda.
"""
import re
from ruamel.yaml.comments import CommentedMap, CommentedSeq
from ruamel.yaml import YAML
environment_filename = 'conda_dev_env.yml'
cmap = CommentedMap()
cmap.yaml_set_start_comment(
'Usage: conda env create -n myenvname -f {} python=3.6'.format(
environment_filename))
cmap['name'] = 'aiida_icl'
cmap['channels'] = CommentedSeq(['conda-forge', 'cjs'])
cmap['channels'].yaml_add_eol_comment('for sqlalchemy-diff and pgtest', 1)
cmap['dependencies'] = dmap = CommentedSeq()
# fix incompatibilities between conda and pypi
replacements = {}
setup_json = get_setup_json()
for base, key in [(None, 'install_requires'),
('extras_require', 'testing'),
('extras_require', 'code_style')]:
requirements = setup_json.get(base, setup_json)[key]
count = 0
for req in sorted(requirements, key=lambda x: x.lower()):
# skip packages required for specific python versions < 3
if re.findall("python_version\\s*\\<\\s*\\'?3", req):
continue
req = req.split(';')[0]
for (regex, replacement) in iter(replacements.items()):
req = re.sub(regex, replacement, req)
count += 1
dmap.append(req.lower())
dmap.yaml_set_comment_before_after_key(len(dmap) - count, before=key)
yaml = YAML(typ='rt')
yaml.default_flow_style = False
yaml.encoding = 'utf-8'
yaml.allow_unicode = True
file_path = os.path.join(ROOT_DIR, environment_filename)
with open(file_path, 'w') as env_file:
yaml.dump(cmap, env_file)
def get_step(tool: Workflow, step_id: str,
loading_context: LoadingContext) -> CommentedMap:
"""Extract a single WorkflowStep for the given step_id."""
extracted = CommentedMap()
step = find_step(tool.steps, step_id, loading_context)[0]
if step is None:
raise Exception(f"Step {step_id} was not found")
new_id, step_name = cast(str, step["id"]).rsplit("#")
extracted["steps"] = CommentedSeq([step])
extracted["inputs"] = CommentedSeq()
extracted["outputs"] = CommentedSeq()
for in_port in cast(List[CWLObjectType], step["in"]):
name = "#" + cast(str, in_port["id"]).split("#")[-1].split("/")[-1]
inp: CWLObjectType = {"id": name, "type": "Any"}
if "default" in in_port:
inp["default"] = in_port["default"]
extracted["inputs"].append(CommentedMap(inp))
in_port["source"] = name
if "linkMerge" in in_port:
del in_port["linkMerge"]
for outport in cast(List[Union[str, Mapping[str, Any]]], step["out"]):
if isinstance(outport, Mapping):
outport_id = cast(str, outport["id"])
else:
outport_id = outport
name = outport_id.split("#")[-1].split("/")[-1]
extracted["outputs"].append({
"id":
name,
"type":
"Any",
"outputSource":
f"{new_id}#{step_name}/{name}",
})
for f in tool.tool:
if f not in ("steps", "inputs", "outputs"):
extracted[f] = tool.tool[f]
extracted["id"] = new_id
if "cwlVersion" not in extracted:
extracted["cwlVersion"] = tool.metadata["cwlVersion"]
return extracted
def __setitem__(self, key: str, value: Any):
if key not in self.yaml_obj:
self.add_subsection(key)
if isinstance(value, (str, int)):
self.yaml_obj[key] = CommentedSeq()
self[key].add_item(value)
elif isinstance(value, dict):
Section(key, self.yaml_obj)
def add_item(self, item: Union[str, int]):
"""Add a new item to the current section
:param item: Receive the value for the current item
"""
if not isinstance(self.yaml_obj, CommentedSeq):
self._get_parent()[self.section_name] = CommentedSeq()
RecipeItem(len(self.yaml_obj), self.yaml_obj, item)
def _resolve_idmap(self,
document, # type: CommentedMap
loader # type: Loader
):
# type: (...) -> None
# Convert fields with mapSubject into lists
# use mapPredicate if the mapped value isn't a dict.
for idmapField in loader.idmap:
if (idmapField in document):
idmapFieldValue = document[idmapField]
if (isinstance(idmapFieldValue, dict)
and "$import" not in idmapFieldValue
and "$include" not in idmapFieldValue):
ls = CommentedSeq()
for k in sorted(idmapFieldValue.keys()):
val = idmapFieldValue[k]
v = None # type: Optional[CommentedMap]
if not isinstance(val, CommentedMap):
if idmapField in loader.mapPredicate:
v = CommentedMap(
((loader.mapPredicate[idmapField], val),))
v.lc.add_kv_line_col(
loader.mapPredicate[idmapField],
document[idmapField].lc.data[k])
v.lc.filename = document.lc.filename
else:
raise validate.ValidationException(
"mapSubject '%s' value '%s' is not a dict"
"and does not have a mapPredicate", k, v)
else:
v = val
v[loader.idmap[idmapField]] = k
v.lc.add_kv_line_col(loader.idmap[idmapField],
document[idmapField].lc.data[k])
v.lc.filename = document.lc.filename
ls.lc.add_kv_line_col(
len(ls), document[idmapField].lc.data[k])
ls.lc.filename = document.lc.filename
ls.append(v)
document[idmapField] = ls
def get_secret_tasks(self, tags=[]):
module_name='k8s_v1_secret'
tasks = CommentedSeq()
for template in self.get_secret_templates():
task = CommentedMap()
task['name'] = 'Create Secret'
task[module_name] = CommentedMap()
task[module_name]['state'] = 'present'
if self._auth:
for key in self._auth:
task[module_name][key] = self._auth[key]
task[module_name]['force'] = template.pop('force', False)
task[module_name]['resource_definition'] = template
if tags:
task['tags'] = copy.copy(tags)
tasks.append(task)
return tasks
def get_pvc_templates(self):
def _volume_to_pvc(claim_name, claim):
template = CommentedMap()
template['force'] = claim.get('force', False)
template['apiVersion'] = 'v1'
template = CommentedMap()
template['apiVersion'] = self.DEFAULT_API_VERSION
template['kind'] = "PersistentVolumeClaim"
template['metadata'] = CommentedMap([
('name', claim_name),
('namespace', self._namespace_name)
])
template['spec'] = CommentedMap()
template['spec']['resources'] = {'requests': {'storage': '1Gi'}}
if claim.get('volume_name'):
template['spec']['volumeName'] = claim['volume_name']
if claim.get('access_modes'):
template['spec']['accessModes'] = claim['access_modes']
if claim.get('requested_storage'):
template['spec']['resources']['requests']['storage'] = claim['requested_storage']
if claim.get('storage_class'):
if not template['metadata'].get('annotations'):
template['metadata']['annotations'] = {}
template['metadata']['annotations']['storageClass'] = claim['storage_class'] #TODO verify this syntax
if claim.get('selector'):
if claim['selector'].get('match_labels'):
if not template['spec'].get('selector'):
template['spec']['selector'] = dict()
template['spec']['selector']['matchLabels'] = claim['match_labels']
if claim['selector'].get('match_expressions'):
if not template['spec'].get('selector'):
template['spec']['selector'] = dict()
template['spec']['selector']['matchExpressions'] = claim['match_expressions']
return template
templates = CommentedSeq()
if self._volumes:
for volname, vol_config in self._volumes.items():
if self.CONFIG_KEY in vol_config:
if vol_config[self.CONFIG_KEY].get('state', 'present') == 'present':
volume = _volume_to_pvc(volname, vol_config[self.CONFIG_KEY])
templates.append(volume)
return templates
def _resolve_type_dsl(self,
document, # type: CommentedMap
loader # type: Loader
):
# type: (...) -> None
for d in loader.type_dsl_fields:
if d in document:
datum2 = datum = document[d]
if isinstance(datum, (str, six.text_type)):
datum2 = self._type_dsl(datum, document.lc.data[
d], document.lc.filename)
elif isinstance(datum, CommentedSeq):
datum2 = CommentedSeq()
for n, t in enumerate(datum):
datum2.lc.add_kv_line_col(
len(datum2), datum.lc.data[n])
datum2.append(self._type_dsl(
t, datum.lc.data[n], document.lc.filename))
if isinstance(datum2, CommentedSeq):
datum3 = CommentedSeq()
seen = [] # type: List[Text]
for i, item in enumerate(datum2):
if isinstance(item, CommentedSeq):
for j, v in enumerate(item):
if v not in seen:
datum3.lc.add_kv_line_col(
len(datum3), item.lc.data[j])
datum3.append(v)
seen.append(v)
else:
if item not in seen:
datum3.lc.add_kv_line_col(
len(datum3), datum2.lc.data[i])
datum3.append(item)
seen.append(item)
document[d] = datum3
else:
document[d] = datum2
def get_deployment_templates(self, default_api=None, default_kind=None, default_strategy=None, engine_state=None):
def _service_to_k8s_container(name, config, container_name=None):
container = CommentedMap()
if container_name:
container['name'] = container_name
else:
container['name'] = container['name'] if config.get('container_name') else name
container['securityContext'] = CommentedMap()
container['state'] = 'present'
volumes = []
for key, value in iteritems(config):
if key in self.IGNORE_DIRECTIVES:
pass
elif key == 'cap_add':
if not container['securityContext'].get('Capabilities'):
container['securityContext']['Capabilities'] = dict(add=[], drop=[])
for cap in value:
if self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap]:
container['securityContext']['Capabilities']['add'].append(
self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap])
elif key == 'cap_drop':
if not container['securityContext'].get('Capabilities'):
container['securityContext']['Capabilities'] = dict(add=[], drop=[])
for cap in value:
if self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap]:
container['securityContext']['Capabilities']['drop'].append(
self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap])
elif key == 'command':
if isinstance(value, string_types):
container['args'] = shlex.split(value)
else:
container['args'] = copy.copy(value)
elif key == 'container_name':
pass
elif key == 'entrypoint':
if isinstance(value, string_types):
container['command'] = shlex.split(value)
else:
container['command'] = copy.copy(value)
elif key == 'environment':
expanded_vars = self.expand_env_vars(value)
if expanded_vars:
if 'env' not in container:
container['env'] = []
container['env'].extend(expanded_vars)
elif key in ('ports', 'expose'):
if not container.get('ports'):
container['ports'] = []
self.add_container_ports(value, container['ports'])
elif key == 'privileged':
container['securityContext']['privileged'] = value
elif key == 'read_only':
container['securityContext']['readOnlyRootFileSystem'] = value
elif key == 'stdin_open':
container['stdin'] = value
elif key == 'volumes':
vols, vol_mounts = self.get_k8s_volumes(value)
if vol_mounts:
if 'volumeMounts' not in container:
container['volumeMounts'] = []
container['volumeMounts'].extend(vol_mounts)
if vols:
volumes += vols
elif key == 'secrets':
for secret, secret_config in iteritems(value):
if self.CONFIG_KEY in secret_config:
vols, vol_mounts, env_variables = self.get_k8s_secrets(secret, secret_config[self.CONFIG_KEY])
if vol_mounts:
if 'volumeMounts' not in container:
container['volumeMounts'] = []
container['volumeMounts'].extend(vol_mounts)
if vols:
volumes += vols
if env_variables:
if 'env' not in container:
container['env'] = []
container['env'].extend(env_variables)
elif key == 'working_dir':
container['workingDir'] = value
else:
container[key] = value
return container, volumes
def _update_volumes(existing_volumes, new_volumes):
existing_names = {}
for vol in existing_volumes:
existing_names[vol['name']] = 1
for vol in new_volumes:
if vol['name'] not in existing_names:
existing_volumes.append(vol)
templates = CommentedSeq()
for name, service_config in iteritems(self._services):
containers = []
volumes = []
pod = {}
if service_config.get('containers'):
for c in service_config['containers']:
cname = "{}-{}".format(name, c['container_name'])
k8s_container, k8s_volumes, = _service_to_k8s_container(name, c, container_name=cname)
containers.append(k8s_container)
_update_volumes(volumes, k8s_volumes)
else:
k8s_container, k8s_volumes = _service_to_k8s_container(name, service_config)
containers.append(k8s_container)
volumes += k8s_volumes
if service_config.get(self.CONFIG_KEY):
for key, value in iteritems(service_config[self.CONFIG_KEY]):
if key == 'deployment':
for deployment_key, deployment_value in iteritems(value):
if deployment_key != 'force':
self.copy_attribute(pod, deployment_key, deployment_value)
labels = CommentedMap([
('app', self._namespace_name),
('service', name)
])
state = service_config.get(self.CONFIG_KEY, {}).get('state', 'present')
if state == 'present':
template = CommentedMap()
template['apiVersion'] = default_api
template['kind'] = default_kind
template['force'] = service_config.get(self.CONFIG_KEY, {}).get('deployment', {}).get('force', False)
template['metadata'] = CommentedMap([
('name', name),
('labels', copy.deepcopy(labels)),
('namespace', self._namespace_name)
])
template['spec'] = CommentedMap()
template['spec']['template'] = CommentedMap()
template['spec']['template']['metadata'] = CommentedMap([('labels', copy.deepcopy(labels))])
template['spec']['template']['spec'] = CommentedMap([
('containers', containers)
])
# When the engine requests a 'stop', set replicas to 0, stopping all containers
template['spec']['replicas'] = 1 if not engine_state == 'stop' else 0
template['spec']['strategy'] = CommentedMap([('type', default_strategy)])
if volumes:
template['spec']['template']['spec']['volumes'] = volumes
if pod:
for key, value in iteritems(pod):
if key == 'securityContext':
template['spec']['template']['spec'][key] = value
elif key != 'replicas' or (key == 'replicas' and engine_state != 'stop'):
# Leave replicas at 0 when engine_state is 'stop'
template['spec'][key] = value
templates.append(template)
return templates
def _init_job(self, joborder, runtime_context):
# type: (Mapping[Text, Text], RuntimeContext) -> Builder
job = cast(Dict[Text, Union[Dict[Text, Any], List[Any], Text, None]],
copy.deepcopy(joborder))
make_fs_access = getdefault(runtime_context.make_fs_access, StdFsAccess)
fs_access = make_fs_access(runtime_context.basedir)
load_listing_req, _ = self.get_requirement(
"LoadListingRequirement")
if load_listing_req is not None:
load_listing = load_listing_req.get("loadListing")
else:
load_listing = "no_listing"
# Validate job order
try:
fill_in_defaults(self.tool[u"inputs"], job, fs_access)
normalizeFilesDirs(job)
schema = self.names.get_name("input_record_schema", "")
if schema is None:
raise WorkflowException("Missing input record schema: "
"{}".format(self.names))
validate.validate_ex(schema, job, strict=False,
logger=_logger_validation_warnings)
if load_listing and load_listing != "no_listing":
get_listing(fs_access, job, recursive=(load_listing == "deep_listing"))
visit_class(job, ("File",), functools.partial(add_sizes, fs_access))
if load_listing == "deep_listing":
for i, inparm in enumerate(self.tool["inputs"]):
k = shortname(inparm["id"])
if k not in job:
continue
v = job[k]
dircount = [0]
def inc(d): # type: (List[int]) -> None
d[0] += 1
visit_class(v, ("Directory",), lambda x: inc(dircount))
if dircount[0] == 0:
continue
filecount = [0]
visit_class(v, ("File",), lambda x: inc(filecount))
if filecount[0] > FILE_COUNT_WARNING:
# Long lines in this message are okay, will be reflowed based on terminal columns.
_logger.warning(strip_dup_lineno(SourceLine(self.tool["inputs"], i, Text).makeError(
"""Recursive directory listing has resulted in a large number of File objects (%s) passed to the input parameter '%s'. This may negatively affect workflow performance and memory use.
If this is a problem, use the hint 'cwltool:LoadListingRequirement' with "shallow_listing" or "no_listing" to change the directory listing behavior:
$namespaces:
cwltool: "http://commonwl.org/cwltool#"
hints:
cwltool:LoadListingRequirement:
loadListing: shallow_listing
""" % (filecount[0], k))))
except (validate.ValidationException, WorkflowException) as err:
raise WorkflowException("Invalid job input record:\n" + Text(err))
files = [] # type: List[Dict[Text, Text]]
bindings = CommentedSeq()
tmpdir = u""
stagedir = u""
docker_req, _ = self.get_requirement("DockerRequirement")
default_docker = None
if docker_req is None and runtime_context.default_container:
default_docker = runtime_context.default_container
if (docker_req or default_docker) and runtime_context.use_container:
if docker_req is not None:
# Check if docker output directory is absolute
if docker_req.get("dockerOutputDirectory") and \
docker_req.get("dockerOutputDirectory").startswith('/'):
outdir = docker_req.get("dockerOutputDirectory")
else:
outdir = docker_req.get("dockerOutputDirectory") or \
runtime_context.docker_outdir or random_outdir()
elif default_docker is not None:
outdir = runtime_context.docker_outdir or random_outdir()
tmpdir = runtime_context.docker_tmpdir or "/tmp"
stagedir = runtime_context.docker_stagedir or "/var/lib/cwl"
else:
outdir = fs_access.realpath(
runtime_context.outdir or tempfile.mkdtemp(
prefix=getdefault(runtime_context.tmp_outdir_prefix,
DEFAULT_TMP_PREFIX)))
if self.tool[u"class"] != 'Workflow':
tmpdir = fs_access.realpath(runtime_context.tmpdir
or tempfile.mkdtemp())
stagedir = fs_access.realpath(runtime_context.stagedir
or tempfile.mkdtemp())
builder = Builder(job,
files,
bindings,
self.schemaDefs,
self.names,
self.requirements,
self.hints,
{},
runtime_context.mutation_manager,
self.formatgraph,
make_fs_access,
fs_access,
runtime_context.job_script_provider,
runtime_context.eval_timeout,
runtime_context.debug,
runtime_context.js_console,
runtime_context.force_docker_pull,
load_listing,
outdir,
tmpdir,
stagedir)
bindings.extend(builder.bind_input(
self.inputs_record_schema, job,
discover_secondaryFiles=getdefault(runtime_context.toplevel, False)))
if self.tool.get("baseCommand"):
for index, command in enumerate(aslist(self.tool["baseCommand"])):
bindings.append({
"position": [-1000000, index],
"datum": command
})
if self.tool.get("arguments"):
for i, arg in enumerate(self.tool["arguments"]):
lc = self.tool["arguments"].lc.data[i]
filename = self.tool["arguments"].lc.filename
bindings.lc.add_kv_line_col(len(bindings), lc)
if isinstance(arg, MutableMapping):
arg = copy.deepcopy(arg)
if arg.get("position"):
arg["position"] = [arg["position"], i]
else:
arg["position"] = [0, i]
bindings.append(arg)
elif ("$(" in arg) or ("${" in arg):
cm = CommentedMap((
("position", [0, i]),
("valueFrom", arg)
))
cm.lc.add_kv_line_col("valueFrom", lc)
cm.lc.filename = filename
bindings.append(cm)
else:
cm = CommentedMap((
("position", [0, i]),
("datum", arg)
))
cm.lc.add_kv_line_col("datum", lc)
cm.lc.filename = filename
bindings.append(cm)
# use python2 like sorting of heterogeneous lists
# (containing str and int types),
if PY3:
key = functools.cmp_to_key(cmp_like_py2)
else: # PY2
key = lambda d: d["position"]
# This awkward construction replaces the contents of
# "bindings" in place (because Builder expects it to be
# mutated in place, sigh, I'm sorry) with its contents sorted,
# supporting different versions of Python and ruamel.yaml with
# different behaviors/bugs in CommentedSeq.
bindings_copy = copy.deepcopy(bindings)
del bindings[:]
bindings.extend(sorted(bindings_copy, key=key))
if self.tool[u"class"] != 'Workflow':
builder.resources = self.evalResources(builder, runtime_context)
return builder
def _init_job(self, joborder, runtimeContext):
# type: (Dict[Text, Text], RuntimeContext) -> Builder
job = cast(Dict[Text, Union[Dict[Text, Any], List[Any], Text, None]],
copy.deepcopy(joborder))
make_fs_access = getdefault(runtimeContext.make_fs_access, StdFsAccess)
fs_access = make_fs_access(runtimeContext.basedir)
# Validate job order
try:
fill_in_defaults(self.tool[u"inputs"], job, fs_access)
normalizeFilesDirs(job)
validate.validate_ex(self.names.get_name("input_record_schema", ""),
job, strict=False, logger=_logger_validation_warnings)
except (validate.ValidationException, WorkflowException) as e:
raise WorkflowException("Invalid job input record:\n" + Text(e))
files = [] # type: List[Dict[Text, Text]]
bindings = CommentedSeq()
tmpdir = u""
stagedir = u""
loadListingReq, _ = self.get_requirement("http://commonwl.org/cwltool#LoadListingRequirement")
if loadListingReq:
loadListing = loadListingReq.get("loadListing")
else:
loadListing = "deep_listing" # will default to "no_listing" in CWL v1.1
dockerReq, _ = self.get_requirement("DockerRequirement")
defaultDocker = None
if dockerReq is None and runtimeContext.default_container:
defaultDocker = runtimeContext.default_container
if (dockerReq or defaultDocker) and runtimeContext.use_container:
if dockerReq:
# Check if docker output directory is absolute
if dockerReq.get("dockerOutputDirectory") and \
dockerReq.get("dockerOutputDirectory").startswith('/'):
outdir = dockerReq.get("dockerOutputDirectory")
else:
outdir = dockerReq.get("dockerOutputDirectory") or \
runtimeContext.docker_outdir or "/var/spool/cwl"
elif defaultDocker:
outdir = runtimeContext.docker_outdir or "/var/spool/cwl"
tmpdir = runtimeContext.docker_tmpdir or "/tmp"
stagedir = runtimeContext.docker_stagedir or "/var/lib/cwl"
else:
outdir = fs_access.realpath(
runtimeContext.outdir or tempfile.mkdtemp(
prefix=getdefault(runtimeContext.tmp_outdir_prefix, DEFAULT_TMP_PREFIX)))
if self.tool[u"class"] != 'Workflow':
tmpdir = fs_access.realpath(runtimeContext.tmpdir or tempfile.mkdtemp())
stagedir = fs_access.realpath(runtimeContext.stagedir or tempfile.mkdtemp())
builder = Builder(job,
files,
bindings,
self.schemaDefs,
self.names,
self.requirements,
self.hints,
runtimeContext.eval_timeout,
runtimeContext.debug,
{},
runtimeContext.js_console,
runtimeContext.mutation_manager,
self.formatgraph,
make_fs_access,
fs_access,
runtimeContext.force_docker_pull,
loadListing,
outdir,
tmpdir,
stagedir,
runtimeContext.job_script_provider)
bindings.extend(builder.bind_input(
self.inputs_record_schema, job,
discover_secondaryFiles=getdefault(runtimeContext.toplevel, False)))
if self.tool.get("baseCommand"):
for n, b in enumerate(aslist(self.tool["baseCommand"])):
bindings.append({
"position": [-1000000, n],
"datum": b
})
if self.tool.get("arguments"):
for i, a in enumerate(self.tool["arguments"]):
lc = self.tool["arguments"].lc.data[i]
fn = self.tool["arguments"].lc.filename
bindings.lc.add_kv_line_col(len(bindings), lc)
if isinstance(a, dict):
a = copy.copy(a)
if a.get("position"):
a["position"] = [a["position"], i]
else:
a["position"] = [0, i]
bindings.append(a)
elif ("$(" in a) or ("${" in a):
cm = CommentedMap((
("position", [0, i]),
("valueFrom", a)
))
cm.lc.add_kv_line_col("valueFrom", lc)
cm.lc.filename = fn
bindings.append(cm)
else:
cm = CommentedMap((
("position", [0, i]),
("datum", a)
))
cm.lc.add_kv_line_col("datum", lc)
cm.lc.filename = fn
bindings.append(cm)
# use python2 like sorting of heterogeneous lists
# (containing str and int types),
# TODO: unify for both runtime
if six.PY3:
key = cmp_to_key(cmp_like_py2)
else: # PY2
key = lambda dict: dict["position"]
bindings.sort(key=key)
if self.tool[u"class"] != 'Workflow':
builder.resources = self.evalResources(builder, runtimeContext)
return builder
def __getitem__(self, key):
val = CommentedSeq.__getitem__(self, key)
return self._evaluate_item(val)
def __init__(self, init=None):
if init is not None:
CommentedSeq.__init__(self, init)
else:
CommentedSeq.__init__(self)
def generate_orchestration_playbook(self, url=None, namespace=None, settings=None, repository_prefix=None,
pull_from_url=None, tag=None, vault_files=None, **kwargs):
"""
Generate an Ansible playbook to orchestrate services.
:param url: registry URL where images were pushed.
:param namespace: registry namespace
:param repository_prefix: prefix to use for the image name
:param settings: settings dict from container.yml
:param pull_from_url: if url to pull from is different than url
:return: playbook dict
"""
def _update_service(service_name, service_config):
if url and namespace:
# Reference previously pushed image
image_id = self.get_latest_image_id_for_service(service_name)
if not image_id:
raise exceptions.AnsibleContainerConductorException(
u"Unable to get image ID for service {}. Did you forget to run "
u"`ansible-container build`?".format(service_name)
)
image_tag = tag or self.get_build_stamp_for_image(image_id)
if repository_prefix:
image_name = "{}-{}".format(repository_prefix, service_name)
elif repository_prefix is None:
image_name = "{}-{}".format(self.project_name, service_name)
else:
image_name = service_name
repository = "{}/{}".format(namespace, image_name)
image_name = "{}:{}".format(repository, image_tag)
pull_url = pull_from_url if pull_from_url else url
service_config['image'] = "{}/{}".format(pull_url.rstrip('/'), image_name)
else:
# We're using a local image, so check that the image was built
image = self.get_latest_image_for_service(service_name)
if image is None:
raise exceptions.AnsibleContainerConductorException(
u"No image found for service {}, make sure you've run `ansible-container "
u"build`".format(service_name)
)
service_config['image'] = image.tags[0]
for service_name, service in iteritems(self.services):
# set the image property of each container
if service.get('containers'):
for container in service['containers']:
if container.get('roles'):
container_service_name = "{}-{}".format(service_name, container['container_name'])
_update_service(container_service_name, container)
else:
container['image'] = container['from']
elif service.get('roles'):
_update_service(service_name, service)
else:
service['image'] = service['from']
play = CommentedMap()
play['name'] = u'Manage the lifecycle of {} on {}'.format(self.project_name, self.display_name)
play['hosts'] = 'localhost'
play['gather_facts'] = 'no'
play['connection'] = 'local'
play['roles'] = CommentedSeq()
play['vars_files'] = CommentedSeq()
play['tasks'] = CommentedSeq()
role = CommentedMap([
('role', 'ansible.kubernetes-modules')
])
if vault_files:
play['vars_files'].extend(vault_files)
play['roles'].append(role)
play.yaml_set_comment_before_after_key(
'roles', before='Include Ansible Kubernetes and OpenShift modules', indent=4)
play.yaml_set_comment_before_after_key('tasks', before='Tasks for setting the application state. '
'Valid tags include: start, stop, restart, destroy', indent=4)
play['tasks'].append(self.deploy.get_namespace_task(state='present', tags=['start']))
play['tasks'].append(self.deploy.get_namespace_task(state='absent', tags=['destroy']))
play['tasks'].extend(self.deploy.get_secret_tasks(tags=['start']))
play['tasks'].extend(self.deploy.get_service_tasks(tags=['start']))
play['tasks'].extend(self.deploy.get_deployment_tasks(engine_state='stop', tags=['stop', 'restart']))
play['tasks'].extend(self.deploy.get_deployment_tasks(tags=['start', 'restart']))
play['tasks'].extend(self.deploy.get_pvc_tasks(tags=['start']))
playbook = CommentedSeq()
playbook.append(play)
logger.debug(u'Created playbook to run project', playbook=playbook)
return playbook
def get_deployment_templates(self, default_api=None, default_kind=None, default_strategy=None, engine_state=None):
def _service_to_container(name, service):
container = CommentedMap()
container['name'] = name
container['securityContext'] = CommentedMap()
container['state'] = 'present'
volumes = []
pod = {}
for key, value in service.items():
if key in self.IGNORE_DIRECTIVES:
pass
elif key == 'cap_add':
if not container['securityContext'].get('Capabilities'):
container['securityContext']['Capabilities'] = dict(add=[], drop=[])
for cap in value:
if self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap]:
container['securityContext']['Capabilities']['add'].append(
self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap])
elif key == 'cap_drop':
if not container['securityContext'].get('Capabilities'):
container['securityContext']['Capabilities'] = dict(add=[], drop=[])
for cap in value:
if self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap]:
container['securityContext']['Capabilities']['drop'].append(
self.DOCKER_TO_KUBE_CAPABILITY_MAPPING[cap])
elif key == 'command':
if isinstance(value, string_types):
container['args'] = shlex.split(value)
else:
container['args'] = value
elif key == 'container_name':
container['name'] = value
elif key == 'entrypoint':
if isinstance(value, string_types):
container['command'] = shlex.split(value)
else:
container['command'] = copy.copy(value)
elif key == 'environment':
expanded_vars = self.expand_env_vars(value)
if expanded_vars:
container['env'] = expanded_vars
elif key in ('ports', 'expose'):
if not container.get('ports'):
container['ports'] = []
self.add_container_ports(value, container['ports'])
elif key == 'privileged':
container['securityContext']['privileged'] = value
elif key == 'read_only':
container['securityContext']['readOnlyRootFileSystem'] = value
elif key == 'stdin_open':
container['stdin'] = value
elif key == 'volumes':
vols, vol_mounts = self.get_k8s_volumes(value)
if vol_mounts:
container['volumeMounts'] = vol_mounts
if vols:
volumes += vols
elif key == 'working_dir':
container['workingDir'] = value
else:
container[key] = value
# Translate options:
if service.get(self.CONFIG_KEY):
for key, value in service[self.CONFIG_KEY].items():
if key == 'deployment':
for deployment_key, deployment_value in value.items():
if deployment_key != 'force':
self.copy_attribute(pod, deployment_key, deployment_value)
return container, volumes, pod
templates = CommentedSeq()
for name, service_config in self._services.items():
container, volumes, pod = _service_to_container(name, service_config)
labels = CommentedMap([
('app', self._namespace_name),
('service', name)
])
state = service_config.get(self.CONFIG_KEY, {}).get('state', 'present')
if state == 'present':
template = CommentedMap()
template['apiVersion'] = default_api
template['kind'] = default_kind
template['force'] = service_config.get(self.CONFIG_KEY, {}).get('deployment', {}).get('force', False)
template['metadata'] = CommentedMap([
('name', name),
('labels', copy.deepcopy(labels)),
('namespace', self._namespace_name)
])
template['spec'] = CommentedMap()
template['spec']['template'] = CommentedMap()
template['spec']['template']['metadata'] = CommentedMap([('labels', copy.deepcopy(labels))])
template['spec']['template']['spec'] = CommentedMap([
('containers', [container]) # TODO: allow multiple pods in a container
])
# When the engine requests a 'stop', set replicas to 0, stopping all containers
template['spec']['replicas'] = 1 if not engine_state == 'stop' else 0
template['spec']['strategy'] = CommentedMap([('type', default_strategy)])
if volumes:
template['spec']['template']['spec']['volumes'] = volumes
if pod:
for key, value in pod.items():
if key == 'securityContext':
template['spec']['template']['spec'][key] = value
elif key != 'replicas' or (key == 'replicas' and engine_state != 'stop'):
# Leave replicas at 0 when engine_state is 'stop'
template['spec'][key] = value
templates.append(template)
return templates