class Config:
def __init__(self, yaml_path=None, key_file_path=None, **kwargs):
self.config_dict = CommentedMap()
for keyword in kwargs:
self.config_dict[keyword] = kwargs[keyword]
if yaml_path is not None:
with open(yaml_path) as config_file:
self.config_dict = yaml.load(config_file, Loader=yaml.Loader)
else:
self.config_dict['columns_to_anonymize'] = {}
if key_file_path is not None:
with open(key_file_path) as key_file:
self.secret_key = key_file.read().strip()
@property
def columns_to_anonymize(self):
return self.config_dict.get('columns_to_anonymize')
@property
def delimiter(self):
return self.config_dict.get('delimiter')
def add_column_config(self, column_name, column_config_dict):
self.config_dict['columns_to_anonymize'][
column_name] = column_config_dict
def save_config(self, save_name=None):
if save_name is None:
from datetime import date
save_name = date.today().strftime('%Y-%m-%d_generated_config.yml')
with open(save_name, 'w') as save_file:
yaml.round_trip_dump(self.config_dict,
save_file,
default_flow_style=False)
def examples(self):
""" Generate EXAMPLES doc string by matching the API version and model name to a YAML file found in
./examples """
result = []
result_str = ''
# check if an example file exists
file_name = self.module_file
example_path = os.path.join(os.path.dirname(__file__), 'examples',
file_name)
if os.path.exists(example_path):
logger.debug('parsing {}'.format(example_path))
yaml_examples = ruamel.yaml.load(
open(example_path, 'r'), Loader=ruamel.yaml.RoundTripLoader)
for ex in yaml_examples['tasks']:
new_example = CommentedMap()
for key, value in ex.items():
if key == 'name':
# Add name as the first key in new_example
new_example['name'] = value
for key, value in ex.items():
if key != 'name':
# Add the module name as the second key
module_name = self.module_file
new_example[module_name] = value
if 'state' in self.helper.argspec:
# Add a state parameter to the example, placing it after the namespace parameter, or name,
# if no namespace.
new_example[module_name] = CommentedMap()
if isinstance(value, type(CommentedMap())):
params = list(value.keys())
i = 0
add_after = 'name'
if 'namespace' in params:
add_after = 'namespace'
if key in ('create', 'patch'):
state = 'present'
elif key == 'replace':
state = 'replaced'
else:
state = 'absent'
while i < len(params):
new_example[module_name][
params[i]] = value[params[i]]
if params[i] == add_after:
new_example[module_name][
'state'] = state
i += 1
if new_example.get('name'):
result.append(new_example)
if len(result):
result_str = ruamel.yaml.dump(result,
Dumper=ruamel.yaml.RoundTripDumper,
width=80)
result_str = re.sub('\n- name:', '\n\n- name:', result_str)
return result_str
def _recursive_set(self, data: CommentedMap, key: str, value: Any) -> None:
key, next_key = self._parse_key(key)
if next_key is not None:
if key not in data:
data[key] = CommentedMap()
next_data = data.get(key, CommentedMap())
return self._recursive_set(next_data, next_key, value)
data[key] = value
def _recursive_set(self, data: CommentedMap, key: str, value: Any) -> None:
if '.' in key:
key, next_key = key.split('.', 1)
if key not in data:
data[key] = CommentedMap()
next_data = data.get(key, CommentedMap())
self._recursive_set(next_data, next_key, value)
return
data[key] = value
def validate_js_expressions(
tool: CommentedMap,
schema: Schema,
jshint_options: Optional[Dict[str, Union[List[str], str, int]]] = None,
container_engine: str = "docker",
) -> None:
if tool.get("requirements") is None:
return
debug = _logger.isEnabledFor(logging.DEBUG)
requirements = tool["requirements"]
default_globals = ["self", "inputs", "runtime", "console"]
for prop in reversed(requirements):
if prop["class"] == "InlineJavascriptRequirement":
expression_lib = prop.get("expressionLib", [])
break
else:
return
js_globals = copy.deepcopy(default_globals)
for i, expression_lib_line in enumerate(expression_lib):
expression_lib_line_errors, expression_lib_line_globals = jshint_js(
expression_lib_line, js_globals, jshint_options, container_engine)
js_globals.extend(expression_lib_line_globals)
print_js_hint_messages(
expression_lib_line_errors,
SourceLine(expression_lib, i, include_traceback=debug),
)
expressions = get_expressions(tool, schema)
for expression, source_line in expressions:
unscanned_str = expression.strip()
try:
scan_slice = scan_expression(unscanned_str)
except SubstitutionError as se:
if source_line:
source_line.raise_type = WorkflowException
raise source_line.makeError(str(se))
else:
raise se
while scan_slice:
if unscanned_str[scan_slice[0]] == "$":
code_fragment = unscanned_str[scan_slice[0] + 1:scan_slice[1]]
code_fragment_js = code_fragment_to_js(code_fragment, "")
expression_errors, _ = jshint_js(code_fragment_js, js_globals,
jshint_options,
container_engine)
print_js_hint_messages(expression_errors, source_line)
unscanned_str = unscanned_str[scan_slice[1]:]
scan_slice = scan_expression(unscanned_str)
def checkversion(
doc: Union[CommentedSeq, CommentedMap],
metadata: CommentedMap,
enable_dev: bool,
) -> Tuple[CommentedMap, str]:
"""Check the validity of the version of the give CWL document.
Returns the document and the validated version string.
"""
cdoc = None # type: Optional[CommentedMap]
if isinstance(doc, CommentedSeq):
if not isinstance(metadata, CommentedMap):
raise Exception("Expected metadata to be CommentedMap")
lc = metadata.lc
metadata = copy.deepcopy(metadata)
metadata.lc.data = copy.copy(lc.data)
metadata.lc.filename = lc.filename
metadata["$graph"] = doc
cdoc = metadata
elif isinstance(doc, CommentedMap):
cdoc = doc
else:
raise Exception("Expected CommentedMap or CommentedSeq")
version = metadata["cwlVersion"]
cdoc["cwlVersion"] = version
updated_from = metadata.get(ORIGINAL_CWLVERSION) or cdoc.get(
ORIGINAL_CWLVERSION)
if updated_from:
if version != INTERNAL_VERSION:
raise ValidationException(
"original_cwlVersion is set (%s) but cwlVersion is '%s', expected '%s' "
% (updated_from, version, INTERNAL_VERSION))
elif version not in UPDATES:
if version in DEVUPDATES:
if enable_dev:
pass
else:
keys = list(UPDATES.keys())
keys.sort()
raise ValidationException(
u"Version '%s' is a development or deprecated version.\n "
"Update your document to a stable version (%s) or use "
"--enable-dev to enable support for development and "
"deprecated versions." % (version, ", ".join(keys)))
else:
raise ValidationException("Unrecognized version %s" % version)
return (cdoc, version)
def format_node(cwl: Union[dict, list, str], node_path=None):
if isinstance(cwl, str):
if len(cwl) > 80:
return Literal(cwl)
else:
return cwl
elif isinstance(cwl, dict):
_fmt_cwl = CommentedMap([
(k, format_node(v, node_path + [k])) for k, v in reorder_node(cwl, node_path)])
if _fmt_cwl.get("class") in ["CommandLineTool", "ExpressionTool", "Workflow"]:
add_space_between_main_sections(_fmt_cwl)
return _fmt_cwl
elif isinstance(cwl, list):
return [format_node(v, node_path) for v in cwl]
else:
return cwl
def _check_properties(
check: str, file: str, path: str, properties: CommentedMap, reference: Dict[str, Any]
) -> bool:
if path:
path += "."
success = True
for key, value in reference.items():
if key not in properties:
c2cciutils.error(
check,
f"The property '{path}{key}' should be defined",
file,
properties.lc.line + 1,
properties.lc.col + 1,
)
success = False
if isinstance(value, dict):
if not isinstance(properties[key], dict):
c2cciutils.error(
check,
f"The property '{path}{key}' should be a dictionary",
file,
properties.lc.line + 1,
properties.lc.col + 1,
)
success = False
else:
success &= _check_properties(check, file, path + key, properties[key], value)
else:
if properties.get(key) != value:
c2cciutils.error(
check,
f"The property '{path}{key}' should have the value, '{value}', "
f"but is '{properties.get(key)}'",
file,
properties.lc.line + 1,
properties.lc.col + 1,
)
success = False
return success
def bind_input(self,
schema, # type: MutableMapping[Text, Any]
datum, # type: Any
discover_secondaryFiles, # type: bool
lead_pos=None, # type: Optional[Union[int, List[int]]]
tail_pos=None, # type: Optional[List[int]]
): # type: (...) -> List[MutableMapping[Text, Any]]
if tail_pos is None:
tail_pos = []
if lead_pos is None:
lead_pos = []
bindings = [] # type: List[MutableMapping[Text, Text]]
binding = None # type: Optional[MutableMapping[Text,Any]]
value_from_expression = False
if "inputBinding" in schema and isinstance(schema["inputBinding"], MutableMapping):
binding = CommentedMap(schema["inputBinding"].items())
assert binding is not None
bp = list(aslist(lead_pos))
if "position" in binding:
bp.extend(aslist(binding["position"]))
else:
bp.append(0)
bp.extend(aslist(tail_pos))
binding["position"] = bp
binding["datum"] = datum
if "valueFrom" in binding:
value_from_expression = True
# Handle union types
if isinstance(schema["type"], MutableSequence):
bound_input = False
for t in schema["type"]:
avsc = None # type: Optional[Schema]
if isinstance(t, string_types) and self.names.has_name(t, ""):
avsc = self.names.get_name(t, "")
elif isinstance(t, MutableMapping) and "name" in t and self.names.has_name(t["name"], ""):
avsc = self.names.get_name(t["name"], "")
if not avsc:
avsc = make_avsc_object(convert_to_dict(t), self.names)
assert avsc is not None
if validate.validate(avsc, datum):
schema = copy.deepcopy(schema)
schema["type"] = t
if not value_from_expression:
return self.bind_input(schema, datum, lead_pos=lead_pos, tail_pos=tail_pos, discover_secondaryFiles=discover_secondaryFiles)
else:
self.bind_input(schema, datum, lead_pos=lead_pos, tail_pos=tail_pos, discover_secondaryFiles=discover_secondaryFiles)
bound_input = True
if not bound_input:
raise validate.ValidationException(u"'%s' is not a valid union %s" % (datum, schema["type"]))
elif isinstance(schema["type"], MutableMapping):
st = copy.deepcopy(schema["type"])
if binding is not None\
and "inputBinding" not in st\
and "type" in st\
and st["type"] == "array"\
and "itemSeparator" not in binding:
st["inputBinding"] = {}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
st[k] = schema[k]
if value_from_expression:
self.bind_input(st, datum, lead_pos=lead_pos, tail_pos=tail_pos, discover_secondaryFiles=discover_secondaryFiles)
else:
bindings.extend(self.bind_input(st, datum, lead_pos=lead_pos, tail_pos=tail_pos, discover_secondaryFiles=discover_secondaryFiles))
else:
if schema["type"] in self.schemaDefs:
schema = self.schemaDefs[schema["type"]]
if schema["type"] == "record":
for f in schema["fields"]:
if f["name"] in datum and datum[f["name"]] is not None:
bindings.extend(self.bind_input(f, datum[f["name"]], lead_pos=lead_pos, tail_pos=f["name"], discover_secondaryFiles=discover_secondaryFiles))
else:
datum[f["name"]] = f.get("default")
if schema["type"] == "array":
for n, item in enumerate(datum):
b2 = None
if binding is not None:
b2 = copy.deepcopy(binding)
b2["datum"] = item
itemschema = {
u"type": schema["items"],
u"inputBinding": b2
}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
itemschema[k] = schema[k]
bindings.extend(
self.bind_input(itemschema, item, lead_pos=n, tail_pos=tail_pos, discover_secondaryFiles=discover_secondaryFiles))
binding = None
def _capture_files(f):
self.files.append(f)
return f
if schema["type"] == "File":
self.files.append(datum)
if (binding and binding.get("loadContents")) or schema.get("loadContents"):
with self.fs_access.open(datum["location"], "rb") as f:
datum["contents"] = f.read(CONTENT_LIMIT).decode("utf-8")
if "secondaryFiles" in schema:
if "secondaryFiles" not in datum:
datum["secondaryFiles"] = []
for sf in aslist(schema["secondaryFiles"]):
if 'required' in sf:
sf_required = self.do_eval(sf['required'], context=datum)
else:
sf_required = True
if "$(" in sf["pattern"] or "${" in sf["pattern"]:
sfpath = self.do_eval(sf["pattern"], context=datum)
else:
sfpath = substitute(datum["basename"], sf["pattern"])
for sfname in aslist(sfpath):
if not sfname:
continue
found = False
for d in datum["secondaryFiles"]:
if not d.get("basename"):
d["basename"] = d["location"][d["location"].rindex("/")+1:]
if d["basename"] == sfname:
found = True
if not found:
sf_location = datum["location"][0:datum["location"].rindex("/")+1]+sfname
if isinstance(sfname, MutableMapping):
datum["secondaryFiles"].append(sfname)
elif discover_secondaryFiles and self.fs_access.exists(sf_location):
datum["secondaryFiles"].append({
"location": sf_location,
"basename": sfname,
"class": "File"})
elif sf_required:
raise WorkflowException("Missing required secondary file '%s' from file object: %s" % (
sfname, json_dumps(datum, indent=4)))
normalizeFilesDirs(datum["secondaryFiles"])
if "format" in schema:
try:
check_format(datum, self.do_eval(schema["format"]),
self.formatgraph)
except validate.ValidationException as ve:
raise WorkflowException(
"Expected value of '%s' to have format %s but\n "
" %s" % (schema["name"], schema["format"], ve))
visit_class(datum.get("secondaryFiles", []), ("File", "Directory"), _capture_files)
if schema["type"] == "Directory":
ll = schema.get("loadListing") or self.loadListing
if ll and ll != "no_listing":
get_listing(self.fs_access, datum, (ll == "deep_listing"))
self.files.append(datum)
if schema["type"] == "Any":
visit_class(datum, ("File", "Directory"), _capture_files)
# Position to front of the sort key
if binding is not None:
for bi in bindings:
bi["position"] = binding["position"] + bi["position"]
bindings.append(binding)
return bindings
def __init__(self, toolpath_object: CommentedMap,
loadingContext: LoadingContext) -> None:
"""Build a Process object from the provided dictionary."""
super(Process, self).__init__()
self.metadata = getdefault(loadingContext.metadata,
{}) # type: CWLObjectType
self.provenance_object = None # type: Optional[ProvenanceProfile]
self.parent_wf = None # type: Optional[ProvenanceProfile]
global SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY # pylint: disable=global-statement
if SCHEMA_FILE is None or SCHEMA_ANY is None or SCHEMA_DIR is None:
get_schema("v1.0")
SCHEMA_ANY = cast(
CWLObjectType,
SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/salad#Any"],
)
SCHEMA_FILE = cast(
CWLObjectType,
SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#File"],
)
SCHEMA_DIR = cast(
CWLObjectType,
SCHEMA_CACHE["v1.0"]
[3].idx["https://w3id.org/cwl/cwl#Directory"],
)
self.names = make_avro_schema([SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY],
Loader({}))
self.tool = toolpath_object
self.requirements = copy.deepcopy(
getdefault(loadingContext.requirements, []))
self.requirements.extend(self.tool.get("requirements", []))
if "id" not in self.tool:
self.tool["id"] = "_:" + str(uuid.uuid4())
self.requirements.extend(
cast(
List[CWLObjectType],
get_overrides(getdefault(loadingContext.overrides_list, []),
self.tool["id"]).get("requirements", []),
))
self.hints = copy.deepcopy(getdefault(loadingContext.hints, []))
self.hints.extend(self.tool.get("hints", []))
# Versions of requirements and hints which aren't mutated.
self.original_requirements = copy.deepcopy(self.requirements)
self.original_hints = copy.deepcopy(self.hints)
self.doc_loader = loadingContext.loader
self.doc_schema = loadingContext.avsc_names
self.formatgraph = None # type: Optional[Graph]
if self.doc_loader is not None:
self.formatgraph = self.doc_loader.graph
checkRequirements(self.tool, supportedProcessRequirements)
self.validate_hints(
cast(Names, loadingContext.avsc_names),
self.tool.get("hints", []),
strict=getdefault(loadingContext.strict, False),
)
self.schemaDefs = {} # type: MutableMapping[str, CWLObjectType]
sd, _ = self.get_requirement("SchemaDefRequirement")
if sd is not None:
sdtypes = cast(MutableSequence[CWLObjectType], sd["types"])
avroize_type(cast(MutableSequence[CWLOutputType], sdtypes))
av = make_valid_avro(
sdtypes,
{
cast(str, t["name"]): cast(Dict[str, Any], t)
for t in sdtypes
},
set(),
)
for i in av:
self.schemaDefs[i["name"]] = i # type: ignore
make_avsc_object(convert_to_dict(av), self.names)
# Build record schema from inputs
self.inputs_record_schema = {
"name": "input_record_schema",
"type": "record",
"fields": [],
} # type: CWLObjectType
self.outputs_record_schema = {
"name": "outputs_record_schema",
"type": "record",
"fields": [],
} # type: CWLObjectType
for key in ("inputs", "outputs"):
for i in self.tool[key]:
c = copy.deepcopy(i)
c["name"] = shortname(c["id"])
del c["id"]
if "type" not in c:
raise ValidationException(
"Missing 'type' in parameter '{}'".format(c["name"]))
if "default" in c and "null" not in aslist(c["type"]):
nullable = ["null"]
nullable.extend(aslist(c["type"]))
c["type"] = nullable
else:
c["type"] = c["type"]
avroize_type(c["type"], c["name"])
if key == "inputs":
cast(List[CWLObjectType],
self.inputs_record_schema["fields"]).append(c)
elif key == "outputs":
cast(List[CWLObjectType],
self.outputs_record_schema["fields"]).append(c)
with SourceLine(toolpath_object, "inputs", ValidationException):
self.inputs_record_schema = cast(
CWLObjectType,
make_valid_avro(self.inputs_record_schema, {}, set()),
)
make_avsc_object(convert_to_dict(self.inputs_record_schema),
self.names)
with SourceLine(toolpath_object, "outputs", ValidationException):
self.outputs_record_schema = cast(
CWLObjectType,
make_valid_avro(self.outputs_record_schema, {}, set()),
)
make_avsc_object(convert_to_dict(self.outputs_record_schema),
self.names)
if toolpath_object.get("class") is not None and not getdefault(
loadingContext.disable_js_validation, False):
validate_js_options = (
None) # type: Optional[Dict[str, Union[List[str], str, int]]]
if loadingContext.js_hint_options_file is not None:
try:
with open(loadingContext.js_hint_options_file
) as options_file:
validate_js_options = json.load(options_file)
except (OSError, ValueError):
_logger.error(
"Failed to read options file %s",
loadingContext.js_hint_options_file,
)
raise
if self.doc_schema is not None:
validate_js_expressions(
toolpath_object,
self.doc_schema.names[toolpath_object["class"]],
validate_js_options,
)
dockerReq, is_req = self.get_requirement("DockerRequirement")
if (dockerReq is not None and "dockerOutputDirectory" in dockerReq
and is_req is not None and not is_req):
_logger.warning(
SourceLine(item=dockerReq, raise_type=str).makeError(
"When 'dockerOutputDirectory' is declared, DockerRequirement "
"should go in the 'requirements' section, not 'hints'."
""))
if (dockerReq is not None and is_req is not None and
dockerReq.get("dockerOutputDirectory") == "/var/spool/cwl"):
if is_req:
# In this specific case, it is legal to have /var/spool/cwl, so skip the check.
pass
else:
# Must be a requirement
var_spool_cwl_detector(self.tool)
else:
var_spool_cwl_detector(self.tool)
def __init__(
self,
toolpath_object: CommentedMap,
pos: int,
loadingContext: LoadingContext,
parentworkflowProv: Optional[ProvenanceProfile] = None,
) -> None:
"""Initialize this WorkflowStep."""
if "id" in toolpath_object:
self.id = toolpath_object["id"]
else:
self.id = "#step" + str(pos)
loadingContext = loadingContext.copy()
loadingContext.requirements = copy.deepcopy(
getdefault(loadingContext.requirements, [])
)
assert loadingContext.requirements is not None # nosec
loadingContext.requirements.extend(toolpath_object.get("requirements", []))
loadingContext.requirements.extend(
cast(
List[CWLObjectType],
get_overrides(
getdefault(loadingContext.overrides_list, []), self.id
).get("requirements", []),
)
)
hints = copy.deepcopy(getdefault(loadingContext.hints, []))
hints.extend(toolpath_object.get("hints", []))
loadingContext.hints = hints
try:
if isinstance(toolpath_object["run"], CommentedMap):
self.embedded_tool = loadingContext.construct_tool_object(
toolpath_object["run"], loadingContext
) # type: Process
else:
loadingContext.metadata = {}
self.embedded_tool = load_tool(toolpath_object["run"], loadingContext)
except ValidationException as vexc:
if loadingContext.debug:
_logger.exception("Validation exception")
raise WorkflowException(
"Tool definition %s failed validation:\n%s"
% (toolpath_object["run"], indent(str(vexc)))
) from vexc
validation_errors = []
self.tool = toolpath_object = copy.deepcopy(toolpath_object)
bound = set()
for stepfield, toolfield in (("in", "inputs"), ("out", "outputs")):
toolpath_object[toolfield] = []
for index, step_entry in enumerate(toolpath_object[stepfield]):
if isinstance(step_entry, str):
param = CommentedMap() # type: CommentedMap
inputid = step_entry
else:
param = CommentedMap(step_entry.items())
inputid = step_entry["id"]
shortinputid = shortname(inputid)
found = False
for tool_entry in self.embedded_tool.tool[toolfield]:
frag = shortname(tool_entry["id"])
if frag == shortinputid:
# if the case that the step has a default for a parameter,
# we do not want the default of the tool to override it
step_default = None
if "default" in param and "default" in tool_entry:
step_default = param["default"]
param.update(tool_entry)
param["_tool_entry"] = tool_entry
if step_default is not None:
param["default"] = step_default
found = True
bound.add(frag)
break
if not found:
if stepfield == "in":
param["type"] = "Any"
param["used_by_step"] = used_by_step(self.tool, shortinputid)
param["not_connected"] = True
else:
if isinstance(step_entry, Mapping):
step_entry_name = step_entry["id"]
else:
step_entry_name = step_entry
validation_errors.append(
SourceLine(self.tool["out"], index).makeError(
"Workflow step output '%s' does not correspond to"
% shortname(step_entry_name)
)
+ "\n"
+ SourceLine(self.embedded_tool.tool, "outputs").makeError(
" tool output (expected '%s')"
% (
"', '".join(
[
shortname(tool_entry["id"])
for tool_entry in self.embedded_tool.tool[
"outputs"
]
]
)
)
)
)
param["id"] = inputid
param.lc.line = toolpath_object[stepfield].lc.data[index][0]
param.lc.col = toolpath_object[stepfield].lc.data[index][1]
param.lc.filename = toolpath_object[stepfield].lc.filename
toolpath_object[toolfield].append(param)
missing_values = []
for _, tool_entry in enumerate(self.embedded_tool.tool["inputs"]):
if shortname(tool_entry["id"]) not in bound:
if "null" not in tool_entry["type"] and "default" not in tool_entry:
missing_values.append(shortname(tool_entry["id"]))
if missing_values:
validation_errors.append(
SourceLine(self.tool, "in").makeError(
"Step is missing required parameter%s '%s'"
% (
"s" if len(missing_values) > 1 else "",
"', '".join(missing_values),
)
)
)
if validation_errors:
raise ValidationException("\n".join(validation_errors))
super().__init__(toolpath_object, loadingContext)
if self.embedded_tool.tool["class"] == "Workflow":
(feature, _) = self.get_requirement("SubworkflowFeatureRequirement")
if not feature:
raise WorkflowException(
"Workflow contains embedded workflow but "
"SubworkflowFeatureRequirement not in requirements"
)
if "scatter" in self.tool:
(feature, _) = self.get_requirement("ScatterFeatureRequirement")
if not feature:
raise WorkflowException(
"Workflow contains scatter but ScatterFeatureRequirement "
"not in requirements"
)
inputparms = copy.deepcopy(self.tool["inputs"])
outputparms = copy.deepcopy(self.tool["outputs"])
scatter = aslist(self.tool["scatter"])
method = self.tool.get("scatterMethod")
if method is None and len(scatter) != 1:
raise ValidationException(
"Must specify scatterMethod when scattering over multiple inputs"
)
inp_map = {i["id"]: i for i in inputparms}
for inp in scatter:
if inp not in inp_map:
raise ValidationException(
SourceLine(self.tool, "scatter").makeError(
"Scatter parameter '%s' does not correspond to "
"an input parameter of this step, expecting '%s'"
% (
shortname(inp),
"', '".join(shortname(k) for k in inp_map.keys()),
)
)
)
inp_map[inp]["type"] = {"type": "array", "items": inp_map[inp]["type"]}
if self.tool.get("scatterMethod") == "nested_crossproduct":
nesting = len(scatter)
else:
nesting = 1
for _ in range(0, nesting):
for oparam in outputparms:
oparam["type"] = {"type": "array", "items": oparam["type"]}
self.tool["inputs"] = inputparms
self.tool["outputs"] = outputparms
self.prov_obj = None # type: Optional[ProvenanceProfile]
if loadingContext.research_obj is not None:
self.prov_obj = parentworkflowProv
if self.embedded_tool.tool["class"] == "Workflow":
self.parent_wf = self.embedded_tool.parent_wf
else:
self.parent_wf = self.prov_obj
def bind_input(
self,
schema: CWLObjectType,
datum: Union[CWLObjectType, List[CWLObjectType]],
discover_secondaryFiles: bool,
lead_pos: Optional[Union[int, List[int]]] = None,
tail_pos: Optional[Union[str, List[int]]] = None,
) -> List[MutableMapping[str, Union[str, List[int]]]]:
debug = _logger.isEnabledFor(logging.DEBUG)
if tail_pos is None:
tail_pos = []
if lead_pos is None:
lead_pos = []
bindings = [] # type: List[MutableMapping[str, Union[str, List[int]]]]
binding = (
{}
) # type: Union[MutableMapping[str, Union[str, List[int]]], CommentedMap]
value_from_expression = False
if "inputBinding" in schema and isinstance(
schema["inputBinding"], MutableMapping
):
binding = CommentedMap(schema["inputBinding"].items())
bp = list(aslist(lead_pos))
if "position" in binding:
position = binding["position"]
if isinstance(position, str): # no need to test the CWL Version
# the schema for v1.0 only allow ints
result = self.do_eval(position, context=datum)
if not isinstance(result, int):
raise SourceLine(
schema["inputBinding"], "position", WorkflowException, debug
).makeError(
"'position' expressions must evaluate to an int, "
f"not a {type(result)}. Expression {position} "
f"resulted in '{result}'."
)
binding["position"] = result
bp.append(result)
else:
bp.extend(aslist(binding["position"]))
else:
bp.append(0)
bp.extend(aslist(tail_pos))
binding["position"] = bp
binding["datum"] = datum
if "valueFrom" in binding:
value_from_expression = True
# Handle union types
if isinstance(schema["type"], MutableSequence):
bound_input = False
for t in schema["type"]:
avsc = None # type: Optional[Schema]
if isinstance(t, str) and self.names.has_name(t, None):
avsc = self.names.get_name(t, None)
elif (
isinstance(t, MutableMapping)
and "name" in t
and self.names.has_name(cast(str, t["name"]), None)
):
avsc = self.names.get_name(cast(str, t["name"]), None)
if not avsc:
avsc = make_avsc_object(convert_to_dict(t), self.names)
if validate(avsc, datum, vocab=INPUT_OBJ_VOCAB):
schema = copy.deepcopy(schema)
schema["type"] = t
if not value_from_expression:
return self.bind_input(
schema,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
else:
self.bind_input(
schema,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
bound_input = True
if not bound_input:
raise ValidationException(
"'{}' is not a valid union {}".format(datum, schema["type"])
)
elif isinstance(schema["type"], MutableMapping):
st = copy.deepcopy(schema["type"])
if (
binding
and "inputBinding" not in st
and "type" in st
and st["type"] == "array"
and "itemSeparator" not in binding
):
st["inputBinding"] = {}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
st[k] = schema[k]
if value_from_expression:
self.bind_input(
st,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
else:
bindings.extend(
self.bind_input(
st,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
)
else:
if schema["type"] == "org.w3id.cwl.salad.Any":
if isinstance(datum, dict):
if datum.get("class") == "File":
schema["type"] = "org.w3id.cwl.cwl.File"
elif datum.get("class") == "Directory":
schema["type"] = "org.w3id.cwl.cwl.Directory"
else:
schema["type"] = "record"
schema["fields"] = [
{"name": field_name, "type": "Any"}
for field_name in datum.keys()
]
elif isinstance(datum, list):
schema["type"] = "array"
schema["items"] = "Any"
if schema["type"] in self.schemaDefs:
schema = self.schemaDefs[cast(str, schema["type"])]
if schema["type"] == "record":
datum = cast(CWLObjectType, datum)
for f in cast(List[CWLObjectType], schema["fields"]):
name = cast(str, f["name"])
if name in datum and datum[name] is not None:
bindings.extend(
self.bind_input(
f,
cast(CWLObjectType, datum[name]),
lead_pos=lead_pos,
tail_pos=name,
discover_secondaryFiles=discover_secondaryFiles,
)
)
else:
datum[name] = f.get("default")
if schema["type"] == "array":
for n, item in enumerate(cast(MutableSequence[CWLObjectType], datum)):
b2 = None
if binding:
b2 = cast(CWLObjectType, copy.deepcopy(binding))
b2["datum"] = item
itemschema = {
"type": schema["items"],
"inputBinding": b2,
} # type: CWLObjectType
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
itemschema[k] = schema[k]
bindings.extend(
self.bind_input(
itemschema,
item,
lead_pos=n,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
)
binding = {}
def _capture_files(f: CWLObjectType) -> CWLObjectType:
self.files.append(f)
return f
if schema["type"] == "org.w3id.cwl.cwl.File":
datum = cast(CWLObjectType, datum)
self.files.append(datum)
loadContents_sourceline = (
None
) # type: Union[None, MutableMapping[str, Union[str, List[int]]], CWLObjectType]
if binding and binding.get("loadContents"):
loadContents_sourceline = binding
elif schema.get("loadContents"):
loadContents_sourceline = schema
if loadContents_sourceline and loadContents_sourceline["loadContents"]:
with SourceLine(
loadContents_sourceline,
"loadContents",
WorkflowException,
debug,
):
try:
with self.fs_access.open(
cast(str, datum["location"]), "rb"
) as f2:
datum["contents"] = content_limit_respected_read(f2)
except Exception as e:
raise Exception(
"Reading {}\n{}".format(datum["location"], e)
)
if "secondaryFiles" in schema:
if "secondaryFiles" not in datum:
datum["secondaryFiles"] = []
sf_schema = aslist(schema["secondaryFiles"])
elif not discover_secondaryFiles:
sf_schema = [] # trust the inputs
else:
sf_schema = aslist(schema["secondaryFiles"])
for num, sf_entry in enumerate(sf_schema):
if "required" in sf_entry and sf_entry["required"] is not None:
required_result = self.do_eval(
sf_entry["required"], context=datum
)
if not (
isinstance(required_result, bool)
or required_result is None
):
if sf_schema == schema["secondaryFiles"]:
sf_item: Any = sf_schema[num]
else:
sf_item = sf_schema
raise SourceLine(
sf_item, "required", WorkflowException, debug
).makeError(
"The result of a expression in the field "
"'required' must "
f"be a bool or None, not a {type(required_result)}. "
f"Expression '{sf_entry['required']}' resulted "
f"in '{required_result}'."
)
sf_required = required_result
else:
sf_required = True
if "$(" in sf_entry["pattern"] or "${" in sf_entry["pattern"]:
sfpath = self.do_eval(sf_entry["pattern"], context=datum)
else:
sfpath = substitute(
cast(str, datum["basename"]), sf_entry["pattern"]
)
for sfname in aslist(sfpath):
if not sfname:
continue
found = False
if isinstance(sfname, str):
d_location = cast(str, datum["location"])
if "/" in d_location:
sf_location = (
d_location[0 : d_location.rindex("/") + 1]
+ sfname
)
else:
sf_location = d_location + sfname
sfbasename = sfname
elif isinstance(sfname, MutableMapping):
sf_location = sfname["location"]
sfbasename = sfname["basename"]
else:
raise SourceLine(
sf_entry, "pattern", WorkflowException, debug
).makeError(
"Expected secondaryFile expression to "
"return type 'str', a 'File' or 'Directory' "
"dictionary, or a list of the same. Received "
f"'{type(sfname)} from '{sf_entry['pattern']}'."
)
for d in cast(
MutableSequence[MutableMapping[str, str]],
datum["secondaryFiles"],
):
if not d.get("basename"):
d["basename"] = d["location"][
d["location"].rindex("/") + 1 :
]
if d["basename"] == sfbasename:
found = True
if not found:
def addsf(
files: MutableSequence[CWLObjectType],
newsf: CWLObjectType,
) -> None:
for f in files:
if f["location"] == newsf["location"]:
f["basename"] = newsf["basename"]
return
files.append(newsf)
if isinstance(sfname, MutableMapping):
addsf(
cast(
MutableSequence[CWLObjectType],
datum["secondaryFiles"],
),
sfname,
)
elif discover_secondaryFiles and self.fs_access.exists(
sf_location
):
addsf(
cast(
MutableSequence[CWLObjectType],
datum["secondaryFiles"],
),
{
"location": sf_location,
"basename": sfname,
"class": "File",
},
)
elif sf_required:
raise SourceLine(
schema,
"secondaryFiles",
WorkflowException,
debug,
).makeError(
"Missing required secondary file '%s' from file object: %s"
% (sfname, json_dumps(datum, indent=4))
)
normalizeFilesDirs(
cast(MutableSequence[CWLObjectType], datum["secondaryFiles"])
)
if "format" in schema:
eval_format: Any = self.do_eval(schema["format"])
if isinstance(eval_format, str):
evaluated_format: Union[str, List[str]] = eval_format
elif isinstance(eval_format, MutableSequence):
for index, entry in enumerate(eval_format):
message = None
if not isinstance(entry, str):
message = (
"An expression in the 'format' field must "
"evaluate to a string, or list of strings. "
"However a non-string item was received: "
f"'{entry}' of type '{type(entry)}'. "
f"The expression was '{schema['format']}' and "
f"its fully evaluated result is '{eval_format}'."
)
if expression.needs_parsing(entry):
message = (
"For inputs, 'format' field can either "
"contain a single CWL Expression or CWL Parameter "
"Reference, a single format string, or a list of "
"format strings. But the list cannot contain CWL "
"Expressions or CWL Parameter References. List "
f"entry number {index+1} contains the following "
"unallowed CWL Parameter Reference or Expression: "
f"'{entry}'."
)
if message:
raise SourceLine(
schema["format"], index, WorkflowException, debug
).makeError(message)
evaluated_format = cast(List[str], eval_format)
else:
raise SourceLine(
schema, "format", WorkflowException, debug
).makeError(
"An expression in the 'format' field must "
"evaluate to a string, or list of strings. "
"However the type of the expression result was "
f"{type(eval_format)}. "
f"The expression was '{schema['format']}' and "
f"its fully evaluated result is 'eval_format'."
)
try:
check_format(
datum,
evaluated_format,
self.formatgraph,
)
except ValidationException as ve:
raise WorkflowException(
"Expected value of '%s' to have format %s but\n "
" %s" % (schema["name"], schema["format"], ve)
) from ve
visit_class(
datum.get("secondaryFiles", []),
("File", "Directory"),
_capture_files,
)
if schema["type"] == "org.w3id.cwl.cwl.Directory":
datum = cast(CWLObjectType, datum)
ll = schema.get("loadListing") or self.loadListing
if ll and ll != "no_listing":
get_listing(
self.fs_access,
datum,
(ll == "deep_listing"),
)
self.files.append(datum)
if schema["type"] == "Any":
visit_class(datum, ("File", "Directory"), _capture_files)
# Position to front of the sort key
if binding:
for bi in bindings:
bi["position"] = cast(List[int], binding["position"]) + cast(
List[int], bi["position"]
)
bindings.append(binding)
return bindings
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 bind_input(
self,
schema: MutableMapping[str, Any],
datum: Any,
discover_secondaryFiles: bool,
lead_pos: Optional[Union[int, List[int]]] = None,
tail_pos: Optional[List[int]] = None,
) -> List[MutableMapping[str, Any]]:
if tail_pos is None:
tail_pos = []
if lead_pos is None:
lead_pos = []
bindings = [] # type: List[MutableMapping[str, str]]
binding = {} # type: Union[MutableMapping[str, str], CommentedMap]
value_from_expression = False
if "inputBinding" in schema and isinstance(schema["inputBinding"],
MutableMapping):
binding = CommentedMap(schema["inputBinding"].items())
bp = list(aslist(lead_pos))
if "position" in binding:
position = binding["position"]
if isinstance(position,
str): # no need to test the CWL Version
# the schema for v1.0 only allow ints
binding["position"] = self.do_eval(position, context=datum)
bp.append(binding["position"])
else:
bp.extend(aslist(binding["position"]))
else:
bp.append(0)
bp.extend(aslist(tail_pos))
binding["position"] = bp
binding["datum"] = datum
if "valueFrom" in binding:
value_from_expression = True
# Handle union types
if isinstance(schema["type"], MutableSequence):
bound_input = False
for t in schema["type"]:
avsc = None # type: Optional[Schema]
if isinstance(t, str) and self.names.has_name(t, ""):
avsc = self.names.get_name(t, "")
elif (isinstance(t, MutableMapping) and "name" in t
and self.names.has_name(t["name"], "")):
avsc = self.names.get_name(t["name"], "")
if not avsc:
avsc = make_avsc_object(convert_to_dict(t), self.names)
if validate.validate(avsc, datum):
schema = copy.deepcopy(schema)
schema["type"] = t
if not value_from_expression:
return self.bind_input(
schema,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
else:
self.bind_input(
schema,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
bound_input = True
if not bound_input:
raise validate.ValidationException(
"'%s' is not a valid union %s" % (datum, schema["type"]))
elif isinstance(schema["type"], MutableMapping):
st = copy.deepcopy(schema["type"])
if (binding and "inputBinding" not in st and "type" in st
and st["type"] == "array"
and "itemSeparator" not in binding):
st["inputBinding"] = {}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
st[k] = schema[k]
if value_from_expression:
self.bind_input(
st,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
)
else:
bindings.extend(
self.bind_input(
st,
datum,
lead_pos=lead_pos,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
))
else:
if schema["type"] in self.schemaDefs:
schema = self.schemaDefs[schema["type"]]
if schema["type"] == "record":
for f in schema["fields"]:
if f["name"] in datum and datum[f["name"]] is not None:
bindings.extend(
self.bind_input(
f,
datum[f["name"]],
lead_pos=lead_pos,
tail_pos=f["name"],
discover_secondaryFiles=discover_secondaryFiles,
))
else:
datum[f["name"]] = f.get("default")
if schema["type"] == "array":
for n, item in enumerate(datum):
b2 = None
if binding:
b2 = copy.deepcopy(binding)
b2["datum"] = item
itemschema = {"type": schema["items"], "inputBinding": b2}
for k in ("secondaryFiles", "format", "streamable"):
if k in schema:
itemschema[k] = schema[k]
bindings.extend(
self.bind_input(
itemschema,
item,
lead_pos=n,
tail_pos=tail_pos,
discover_secondaryFiles=discover_secondaryFiles,
))
binding = {}
def _capture_files(f): # type: (Dict[str, str]) -> Dict[str, str]
self.files.append(f)
return f
if schema["type"] == "File":
self.files.append(datum)
if (binding and binding.get("loadContents")
) or schema.get("loadContents"):
with self.fs_access.open(datum["location"], "rb") as f:
datum["contents"] = content_limit_respected_read(f)
if "secondaryFiles" in schema:
if "secondaryFiles" not in datum:
datum["secondaryFiles"] = []
for sf in aslist(schema["secondaryFiles"]):
if "required" in sf:
sf_required = self.do_eval(sf["required"],
context=datum)
else:
sf_required = True
if "$(" in sf["pattern"] or "${" in sf["pattern"]:
sfpath = self.do_eval(sf["pattern"], context=datum)
else:
sfpath = substitute(datum["basename"],
sf["pattern"])
for sfname in aslist(sfpath):
if not sfname:
continue
found = False
if isinstance(sfname, str):
sf_location = (
datum["location"]
[0:datum["location"].rindex("/") + 1] +
sfname)
sfbasename = sfname
elif isinstance(sfname, MutableMapping):
sf_location = sfname["location"]
sfbasename = sfname["basename"]
else:
raise WorkflowException(
"Expected secondaryFile expression to return type 'str' or 'MutableMapping', received '%s'"
% (type(sfname)))
for d in datum["secondaryFiles"]:
if not d.get("basename"):
d["basename"] = d["location"][
d["location"].rindex("/") + 1:]
if d["basename"] == sfbasename:
found = True
if not found:
def addsf(
files: MutableSequence[MutableMapping[
str, Any]],
newsf: MutableMapping[str, Any],
) -> None:
for f in files:
if f["location"] == newsf["location"]:
f["basename"] = newsf["basename"]
return
files.append(newsf)
if isinstance(sfname, MutableMapping):
addsf(datum["secondaryFiles"], sfname)
elif discover_secondaryFiles and self.fs_access.exists(
sf_location):
addsf(
datum["secondaryFiles"],
{
"location": sf_location,
"basename": sfname,
"class": "File",
},
)
elif sf_required:
raise WorkflowException(
"Missing required secondary file '%s' from file object: %s"
%
(sfname, json_dumps(datum, indent=4)))
normalizeFilesDirs(datum["secondaryFiles"])
if "format" in schema:
try:
check_format(datum, self.do_eval(schema["format"]),
self.formatgraph)
except validate.ValidationException as ve:
raise WorkflowException(
"Expected value of '%s' to have format %s but\n "
" %s" %
(schema["name"], schema["format"], ve)) from ve
visit_class(
datum.get("secondaryFiles", []),
("File", "Directory"),
_capture_files,
)
if schema["type"] == "Directory":
ll = schema.get("loadListing") or self.loadListing
if ll and ll != "no_listing":
get_listing(self.fs_access, datum, (ll == "deep_listing"))
self.files.append(datum)
if schema["type"] == "Any":
visit_class(datum, ("File", "Directory"), _capture_files)
# Position to front of the sort key
if binding:
for bi in bindings:
bi["position"] = binding["position"] + bi["position"]
bindings.append(binding)
return bindings
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
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
def _recursive_get(self, data: CommentedMap, key: str, default_value: Any) -> Any:
key, next_key = self._parse_key(key)
if next_key is not None:
next_data = data.get(key, CommentedMap())
return self._recursive_get(next_data, next_key, default_value)
return data.get(key, default_value)
def main(docname):
with open(docname, "r") as fi:
lines = fi.readlines()
context = {}
rest_lines = []
for line in lines:
# print(line)
if "{%" in line:
set_expr = re.search("{%(.*)%}", line)
set_expr = set_expr.group(1)
set_expr = set_expr.replace("set", "", 1).strip()
exec(set_expr, globals(), context)
else:
rest_lines.append(line)
yaml = YAML(typ="rt")
yaml.preserve_quotes = True
yaml.default_flow_style = False
yaml.indent(sequence=4, offset=2)
yaml.width = 1000
yaml.Representer = MyRepresenter
yaml.Loader = ruamel.yaml.RoundTripLoader
result_yaml = CommentedMap()
result_yaml["context"] = context
def has_selector(s):
return s.strip().endswith("]")
quoted_lines = []
for line in rest_lines:
if has_selector(line):
selector_start = line.rfind("[")
selector_end = line.rfind("]")
selector_content = line[selector_start + 1 : selector_end]
if line.strip().startswith("-"):
line = (
line[: line.find("-") + 1]
+ f" sel({selector_content}): "
+ line[
line.find("-") + 1 : min(line.rfind("#"), line.rfind("["))
].strip()
+ "\n"
)
quoted_lines.append(line)
rest_lines = quoted_lines
def check_if_quoted(s):
s = s.strip()
return s.startswith('"') or s.startswith("'")
quoted_lines = []
for line in rest_lines:
if "{{" in line:
# make sure that jinja stuff is quoted
if line.find(":") != -1:
idx = line.find(":")
elif line.strip().startswith("-"):
idx = line.find("-")
rest = line[idx + 1 :]
if not check_if_quoted(rest):
if "'" in rest:
rest = rest.replace("'", '"')
line = line[: idx + 1] + f" '{rest.strip()}'\n"
quoted_lines.append(line)
rest_lines = quoted_lines
skips, wo_skip_lines = [], []
for line in rest_lines:
if line.strip().startswith("skip"):
parts = line.split(":")
rhs = parts[1].strip()
if rhs.startswith("true"):
selector_start = line.rfind("[")
selector_end = line.rfind("]")
selector_content = line[selector_start + 1 : selector_end]
skips.append(selector_content)
else:
print("ATTENTION skip: false not handled!")
else:
wo_skip_lines.append(line)
rest_lines = wo_skip_lines
result_yaml.update(
ruamel.yaml.load("".join(rest_lines), ruamel.yaml.RoundTripLoader)
)
if len(skips) != 0:
result_yaml["build"]["skip"] = skips
if result_yaml.get("outputs"):
for o in result_yaml["outputs"]:
name = o["name"]
package = {"name": name}
del o["name"]
if o.get("version"):
package["version"] = o["version"]
del o["version"]
build = {}
if o.get("script"):
build["script"] = o["script"]
del o["script"]
o["package"] = package
o["build"] = build
for d in result_yaml["outputs"]:
print(order_output_dict(d))
result_yaml["outputs"] = [order_output_dict(d) for d in result_yaml["outputs"]]
from io import StringIO
output = StringIO()
yaml.dump(result_yaml, output)
# Hacky way to insert an empty line after the context-key-object
context_output = StringIO()
yaml.dump(context, context_output)
context_output = context_output.getvalue()
context_output_len = len(context_output.split("\n"))
final_result = output.getvalue()
final_result_lines = final_result.split("\n")
final_result_lines.insert(context_output_len, "")
print("\n".join(final_result_lines))
class RootManifest:
"""
Manifest: defaults to the "vault.yml" file in
the current directory.
"""
def __init__(self, path: str = None, load: bool = True):
self.path = os.path.abspath(path) if path else None
self._backing = CommentedMap()
if load:
self._load()
self._changes = deepcopy(self._backing)
def _load(self):
if os.path.exists(self.path):
with open(self.path, mode="r") as f:
self._backing.update(yaml.safe_load(f))
def set_header(self, header: str) -> None:
self._header = header
def create_secrets_backend_section(self) -> None:
if "secrets_backends" not in self._changes:
self._changes["secrets_backends"] = {}
self._changes.yaml_set_comment_before_after_key(
"secrets_backends",
before=
"Secrets backends. Each key is the mount to a secrets engine.")
def add_secrets_backend(self, name: str, manifest: ManifestItem) -> None:
converted = manifest.convert()
if not converted:
return
name = name.strip("/")
new_dict = self._changes["secrets_backends"].get(name, {})
new_dict.update(converted)
self._changes["secrets_backends"][name] = new_dict
def delete_secrets_backend(self, name: str) -> None:
name = name.strip("/")
if "secrets_backends" in self._changes and name in self._changes[
"secrets_backends"]:
del self._changes["secrets_backends"][name]
def list_secrets_backend_names(self) -> List[str]:
return [
name.strip("/")
for name in self._backing.get("secrets_backends", {})
]
def create_auth_method_section(self) -> None:
if "auth_methods" not in self._changes:
self._changes["auth_methods"] = {}
self._changes.yaml_set_comment_before_after_key(
"auth_methods",
before=
"Authentication methods. Each key is the name of the auth method."
)
def add_auth_method(self, name: str, manifest: ManifestItem) -> None:
converted = manifest.convert()
if not converted:
return
if "auth_methods" not in self._changes:
self._changes["auth_methods"] = {}
name = name.strip("/")
new_dict = self._changes["auth_methods"].get(name, {})
new_dict.update(converted)
self._changes["auth_methods"][name] = new_dict
def yaml(self) -> str:
output = ""
if self._header:
for line in self._header.split("\n"):
output += f"# {line}\n"
output += "\n"
output += yaml.round_trip_dump(self._changes)
return output
def save(self) -> None:
with open(self.path, "w") as f:
f.write(self.yaml())
class YAMLRoundtripConfig(MutableConfigFile, MutableAbstractItemAccessMixin, MutableAbstractDictFunctionsMixin):
"""
Class for YAML-based (roundtrip) configurations
"""
def __init__(self, owner: Any, manager: "m.StorageManager", path: str, *args: List[Any], **kwargs: Dict[Any, Any]):
self.data = CommentedMap()
super().__init__(owner, manager, path, *args, **kwargs)
def load(self):
with open(self.path, "r") as fh:
self.data = yaml.round_trip_load(fh, version=(1, 2))
def reload(self):
self.unload()
self.load()
def unload(self):
self.data.clear()
def save(self):
if not self.mutable:
raise RuntimeError("You may not modify a defaults file at runtime - check the mutable attribute!")
with open(self.path, "w") as fh:
yaml.round_trip_dump(self.data, fh)
# region: CommentedMap functions
def insert(self, pos, key, value, *, comment=None):
"""
Insert a `key: value` pair at the given position, attaching a comment if provided
Wrapper for `CommentedMap.insert()`
"""
return self.data.insert(pos, key, value, comment)
def add_eol_comment(self, comment, *, key=NoComment, column=30):
"""
Add an end-of-line comment for a key at a particular column (30 by default)
Wrapper for `CommentedMap.yaml_add_eol_comment()`
"""
# Setting the column to None as the API actually defaults to will raise an exception, so we have to
# specify one unfortunately
return self.data.yaml_add_eol_comment(comment, key=key, column=column)
def set_comment_before_key(self, key, comment, *, indent=0):
"""
Set a comment before a given key
Wrapper for `CommentedMap.yaml_set_comment_before_after_key()`
"""
return self.data.yaml_set_comment_before_after_key(
key, before=comment, indent=indent, after=None, after_indent=None
)
def set_start_comment(self, comment, indent=0):
"""
Set the starting comment
Wrapper for `CommentedMap.yaml_set_start_comment()`
"""
return self.data.yaml_set_start_comment(comment, indent=indent)
# endregion
# region: Dict functions
def clear(self):
return self.data.clear()
def copy(self):
return self.data.copy()
def get(self, key, default=None):
return self.data.get(key, default)
def items(self):
return self.data.items()
def keys(self):
return self.data.keys()
def pop(self, key, default=None):
return self.data.pop(key, default)
def popitem(self):
return self.data.popitem()
def setdefault(self, key, default=None):
if key not in self.data:
self.data[key] = default
return default
return self.data[key]
def update(self, other):
return self.data.update(other)
def values(self):
return self.data.values()
# endregion
# Item access functions
def __contains__(self, key):
"""
Wrapper for `dict.__contains__()`
"""
return self.data.__contains__(key)
def __delitem__(self, key):
"""
Wrapper for `dict.__delitem__()`
"""
del self.data[key]
def __getitem__(self, key):
"""
Wrapper for `dict.__getitem__()`
"""
return self.data.__getitem__(key)
def __iter__(self):
"""
Wrapper for `dict.__iter__()`
"""
return self.data.__iter__()
def __len__(self):
"""
Wrapper for `dict.__len__()`
"""
return self.data.__len__()
def __setitem__(self, key, value):
"""
Wrapper for `dict.__getitem__()`
"""
return self.data.__setitem__(key, value)
def _recursive_get(self, data: CommentedMap, key: str, default_value: Any) -> Any:
if '.' in key:
key, next_key = key.split('.', 1)
next_data = data.get(key, CommentedMap())
return self._recursive_get(next_data, next_key, default_value)
return data.get(key, default_value)
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