code string | signature string | docstring string | loss_without_docstring float64 | loss_with_docstring float64 | factor float64 |
|---|---|---|---|---|---|
self.append_volume(runtime, volume.resolved, volume.target,
writable=True)
else:
if host_outdir_tgt:
# shortcut, just copy to the output directory
# which is already going to be mounted
if not os.path.exists(o... | def add_writable_file_volume(self,
runtime, # type: List[Text]
volume, # type: MapperEnt
host_outdir_tgt, # type: Optional[Text]
tmpdir_prefix # type: Text
... | Append a writable file mapping to the runtime option list. | 2.973884 | 2.772563 | 1.072612 |
# Synthetic directory that needs creating first
if not host_outdir_tgt:
tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
new_dir = os.path.join(
tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir),
os.path.basename(volume.tar... | def add_writable_directory_volume(self,
runtime, # type: List[Text]
volume, # type: MapperEnt
host_outdir_tgt, # type: Optional[Text]
tmpdir_prefix ... | Append a writable directory mapping to the runtime option list. | 2.15505 | 2.24123 | 0.961548 |
load = load_tool.load_tool(cwl, self.loading_context)
if isinstance(load, int):
raise Exception("Error loading tool")
return Callable(load, self) | def make(self, cwl) | Instantiate a CWL object from a CWl document. | 9.447151 | 8.99241 | 1.050569 |
optional = False
if 'null' in inptype:
inptype.remove('null')
optional = True
if len(inptype) == 1:
example, comment = generate_example_input(inptype[0], default)
if optional:
if comment:
comment = u"{} (optional... | def generate_example_input(inptype, # type: Any
default # type: Optional[Any]
): # type: (...) -> Tuple[Any, Text]
example = None
comment = u""
defaults = {u'null': 'null',
u'Any': 'null',
u'boolean': False,
... | Converts a single input schema into an example. | 2.106876 | 2.063619 | 1.020961 |
if isinstance(entry, string_types):
if '#' in entry:
_, input_type_name = entry.split('#')
else:
input_type_name = entry
if input_type_name in schema_defs:
entry = input_types[index] = schema_defs[input_type_name]
if isi... | def realize_input_schema(input_types, # type: MutableSequence[Dict[Text, Any]]
schema_defs # type: Dict[Text, Any]
): # type: (...) -> MutableSequence[Dict[Text, Any]]
for index, entry in enumerate(input_types) | Replace references to named typed with the actual types. | 1.839013 | 1.763735 | 1.042681 |
# type: (Process) -> Dict[Text, Any]
template = yaml.comments.CommentedMap()
for inp in realize_input_schema(tool.tool["inputs"], tool.schemaDefs):
name = shortname(inp["id"])
value, comment = generate_example_input(
inp['type'], inp.get('default', None))
template.in... | def generate_input_template(tool) | Generate an example input object for the given CWL process. | 7.278247 | 6.29298 | 1.156566 |
uri = obj.get("location", obj.get("path"))
if ":" in uri.split("/")[0] and not uri.startswith("file://"):
pass
else:
if uri.startswith("file://"):
uri = uri_file_path(uri)
obj["location"] = os.path.relpath(uri, base) | def make_relative(base, obj) | Relativize the location URI of a File or Directory object. | 4.116307 | 3.696947 | 1.113434 |
base = basedir if basedir else os.path.dirname(uri_file_path(str(uri)))
elif relative_deps == "cwd":
base = os.getcwd()
visit_class(deps, ("File", "Directory"), functools.partial(
make_relative, base))
stdout.write(json_dumps(deps, indent=4)) | def printdeps(obj, # type: Mapping[Text, Any]
document_loader, # type: Loader
stdout, # type: Union[TextIO, StreamWriter]
relative_deps, # type: bool
uri, # type: Text
basedir=None, # type: Text
... | Print a JSON representation of the dependencies of the CWL document. | 6.402553 | 5.893164 | 1.086437 |
return document_loader.fetch(document_loader.fetcher.urljoin(base, uri))
sfs = scandeps(
basedir if basedir else uri, obj, {"$import", "run"},
{"$include", "$schemas", "location"}, loadref, nestdirs=nestdirs)
if sfs is not None:
deps["secondaryFiles"] = sfs
return deps | def find_deps(obj, # type: Mapping[Text, Any]
document_loader, # type: Loader
uri, # type: Text
basedir=None, # type: Text
nestdirs=True # type: bool
): # type: (...) -> Dict[Text, Any]
deps = {"class": "Fi... | Find the dependencies of the CWL document. | 6.033099 | 6.139338 | 0.982695 |
return json_dumps(packed, indent=4)
return json_dumps(packed["$graph"][0], indent=4) | def print_pack(document_loader, # type: Loader
processobj, # type: CommentedMap
uri, # type: Text
metadata # type: Dict[Text, Any]
): # type (...) -> Text
packed = pack(document_loader, processobj, uri, metadata)
if le... | Return a CWL serialization of the CWL document in JSON. | 3.555724 | 3.23725 | 1.098378 |
default_container = get_container_from_software_requirements(
use_biocontainers, builder)
return default_container | def find_default_container(builder, # type: HasReqsHints
default_container=None, # type: Text
use_biocontainers=None, # type: bool
): # type: (...) -> Optional[Text]
if not default_container and use_biocontaine... | Default finder for default containers. | 10.447235 | 6.332307 | 1.649831 |
# type: (...) -> None
signal.signal(signal.SIGTERM, _signal_handler)
try:
sys.exit(main(*args, **kwargs))
finally:
_terminate_processes() | def run(*args, **kwargs) | Run cwltool. | 4.073208 | 3.92281 | 1.038339 |
raise Exception("Secret store only accepts strings")
if value not in self.secrets:
placeholder = "(secret-%s)" % Text(uuid.uuid4())
self.secrets[placeholder] = value
return placeholder
return value | def add(self, value): # type: (Text) -> Text
if not isinstance(value, string_types) | Add the given value to the store.
Returns a placeholder value to use until the real value is needed. | 9.827287 | 7.405854 | 1.326962 |
# type: (List[Text], MutableMapping[Text, Any]) -> None
for j in job:
if j in secrets:
job[j] = self.add(job[j]) | def store(self, secrets, job) | Sanitize the job object of any of the given secrets. | 5.693315 | 4.804946 | 1.184886 |
for k in self.secrets:
if k in value:
return True
elif isinstance(value, MutableMapping):
for this_value in value.values():
if self.has_secret(this_value):
return True
elif isinstance(value, MutableSequence):... | def has_secret(self, value): # type: (Any) -> bool
if isinstance(value, string_types) | Test if the provided document has any of our secrets. | 2.275934 | 2.020026 | 1.126685 |
for key, this_value in self.secrets.items():
value = value.replace(key, this_value)
elif isinstance(value, MutableMapping):
return {k: self.retrieve(v) for k, v in value.items()}
elif isinstance(value, MutableSequence):
return [self.retrieve(v) for k, ... | def retrieve(self, value): # type: (Any) -> Any
if isinstance(value, string_types) | Replace placeholders with their corresponding secrets. | 2.865964 | 2.212635 | 1.295272 |
# type: () -> Tuple[Text,Text]
username = getuser()
try:
if onWindows():
get_user_name = ctypes.windll.secur32.GetUserNameExW # type: ignore
size = ctypes.pointer(ctypes.c_ulong(0))
get_user_name(3, None, size)
name_buffer = ctypes.create_unicod... | def _whoami() | Return the current operating system account as (username, fullname). | 3.082693 | 2.793751 | 1.103424 |
# type: (Text) -> bool
# Strip -
nums = numeric_string.replace("-", "")
total = 0
# skip last (check)digit
for num in nums[:-1]:
digit = int(num)
total = (total+digit)*2
remainder = total % 11
result = (12-remainder) % 11
if result == 10:
checkdigit = "X"... | def _check_mod_11_2(numeric_string) | Validate numeric_string for its MOD-11-2 checksum.
Any "-" in the numeric_string are ignored.
The last digit of numeric_string is assumed to be the checksum, 0-9 or X.
See ISO/IEC 7064:2003 and
https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier | 4.28021 | 4.45548 | 0.960662 |
raise ValueError(u'ORCID cannot be unspecified')
# Liberal in what we consume, e.g. ORCID.org/0000-0002-1825-009x
orcid = orcid.lower()
match = re.match(
# Note: concatinated r"" r"" below so we can add comments to pattern
# Optional hostname, with or without protocol
r"(htt... | def _valid_orcid(orcid): # type: (Optional[Text]) -> Text
if orcid is None or not orcid | Ensure orcid is a valid ORCID identifier.
The string must be equivalent to one of these forms:
0000-0002-1825-0097
orcid.org/0000-0002-1825-0097
http://orcid.org/0000-0002-1825-0097
https://orcid.org/0000-0002-1825-0097
If the ORCID number or prefix is invalid, a ValueError is raised.
Th... | 5.22257 | 5.058656 | 1.032403 |
temp_location = os.path.join(os.path.dirname(dst_file.name),
str(uuid.uuid4()))
try:
os.rename(dst_file.name, temp_location)
os.link(src_file.name, dst_file.name)
dst_file = None
os.unlink(temp_location)
except ... | def checksum_copy(src_file, # type: IO
dst_file=None, # type: Optional[IO]
hasher=Hasher, # type: Callable[[], Any]
buffersize=1024*1024 # type: int
): # type: (...) -> str
# TODO: Use hashlib.new(Hasher_str) instead... | Compute checksums while copying a file. | 2.081784 | 2.076236 | 1.002673 |
# type: (Any, Any) -> Any
if not hasattr(job, "tool"):
# direct command line tool execution
return job_order_object
customised_job = {} # new job object for RO
for each, i in enumerate(job.tool["inputs"]):
with SourceLine(job.tool["inputs"], each, WorkflowException,
... | def copy_job_order(job, job_order_object) | Create copy of job object for provenance. | 5.46123 | 5.191853 | 1.051885 |
# record provenance of independent commandline tool executions
self.prospective_prov(job)
customised_job = copy_job_order(job, job_order_object)
self.used_artefacts(customised_job, self.workflow_run_uri)
research_obj.create_job(customised_job, job)
eli... | def evaluate(self,
process, # type: Process
job, # type: Any
job_order_object, # type: Dict[Text, Text]
research_obj # type: ResearchObject
): # type: (...) -> None
if not hasattr(process... | Evaluate the nature of job | 4.956556 | 4.875307 | 1.016665 |
# type: (Text, datetime.datetime, Optional[str]) -> str
if process_run_id is None:
process_run_id = uuid.uuid4().urn
prov_label = "Run of workflow/packed.cwl#main/" + process_name
self.document.activity(
process_run_id, None, None,
{provM.PROV... | def start_process(self, process_name, when, process_run_id=None) | Record the start of each Process. | 4.348245 | 4.33716 | 1.002556 |
# type: (Union[Text, str]) -> Tuple[ProvEntity,Text]
byte_s = BytesIO(str(value).encode(ENCODING))
data_file = self.research_object.add_data_file(byte_s, content_type=TEXT_PLAIN)
checksum = posixpath.basename(data_file)
# FIXME: Don't naively assume add_data_file uses ha... | def declare_string(self, value) | Save as string in UTF-8. | 7.314722 | 7.363397 | 0.99339 |
base += "/" + name
for key, value in job_order.items():
prov_role = self.wf_ns["%s/%s" % (base, key)]
entity = self.declare_artefact(value)
self.document.used(
process_run_id, entity, datetime.datetime.now(), None,
{"prov:role": pro... | def used_artefacts(self,
job_order, # type: Dict
process_run_id, # type: str
name=None # type: str
): # type: (...) -> None
# FIXME: Use workflow name in packed.cwl, "main" is wrong ... | Add used() for each data artefact. | 7.318515 | 6.001051 | 1.219539 |
entity = self.declare_artefact(value)
if name is not None:
name = urllib.parse.quote(str(name), safe=":/,#")
# FIXME: Probably not "main" in nested workflows
role = self.wf_ns["main/%s/%s" % (name, output)]
else:
role = ... | def generate_output_prov(self,
final_output, # type: Dict[Text, Any]
process_run_id, # type: Optional[str]
name # type: Optional[Text]
): # type: (...) -> None
# Timestam... | Call wasGeneratedBy() for each output,copy the files into the RO. | 5.904745 | 5.462313 | 1.080997 |
# type: (Any) -> None
if not hasattr(job, "steps"):
# direct command line tool execution
self.document.entity(
"wf:main", {provM.PROV_TYPE: WFDESC["Process"],
"prov:type": PROV["Plan"],
"prov:label":... | def prospective_prov(self, job) | Create prospective prov recording as wfdesc prov:Plan. | 3.875356 | 3.536282 | 1.095884 |
# type: (str, List[Identifier]) -> None
# NOTE: The below will only work if the corresponding metadata/provenance arcp URI
# is a pre-registered namespace in the PROV Document
attribs = [(PROV["has_provenance"], prov_id) for prov_id in prov_ids]
self.document.activity(ac... | def activity_has_provenance(self, activity, prov_ids) | Add http://www.w3.org/TR/prov-aq/ relations to nested PROV files. | 9.738184 | 9.482772 | 1.026934 |
# type: (Optional[Text]) -> List[Identifier]
# NOTE: Relative posix path
if name is None:
# master workflow, fixed filenames
filename = "primary.cwlprov"
else:
# ASCII-friendly filename, avoiding % as we don't want %2520 in manifest.json
... | def finalize_prov_profile(self, name) | Transfer the provenance related files to the RO. | 3.173836 | 3.170161 | 1.001159 |
# TODO: \n or \r\n ?
bag_it_file.write(u"BagIt-Version: 0.97\n")
bag_it_file.write(u"Tag-File-Character-Encoding: %s\n" % ENCODING) | def _initialize_bagit(self): # type: () -> None
self.self_check()
bagit = os.path.join(self.folder, "bagit.txt")
# encoding: always UTF-8 (although ASCII would suffice here)
# newline: ensure LF also on Windows
with open(bagit, "w", encoding=ENCODING, newline='\n') as b... | Write fixed bagit header. | 2.586115 | 2.307371 | 1.120806 |
self.full_name = fullname
document.add_namespace(UUID)
document.add_namespace(ORCID)
document.add_namespace(FOAF)
account = document.agent(
ACCOUNT_UUID, {provM.PROV_TYPE: FOAF["OnlineAccount"],
"prov:label": username,
... | def user_provenance(self, document): # type: (ProvDocument) -> None
self.self_check()
(username, fullname) = _whoami()
if not self.full_name | Add the user provenance. | 7.217757 | 6.901415 | 1.045837 |
# type: (Text, Optional[str]) -> IO
self.self_check()
# For some reason below throws BlockingIOError
#fp = BufferedWriter(WritableBagFile(self, path))
bag_file = cast(IO, WritableBagFile(self, path))
if encoding is not None:
# encoding: match Tag-File... | def write_bag_file(self, path, encoding=ENCODING) | Write the bag file into our research object. | 9.750151 | 9.822235 | 0.992661 |
# type: (Text, datetime.datetime) -> None
self.self_check()
checksums = {}
# Read file to calculate its checksum
if os.path.isdir(path):
return
# FIXME: do the right thing for directories
with open(path, "rb") as tag_file:
# FI... | def add_tagfile(self, path, timestamp=None) | Add tag files to our research object. | 4.725503 | 4.677817 | 1.010194 |
# type: (str, List[str], str) -> str
self.self_check()
curr = self.base_uri + METADATA + "/"
content = [c.replace(curr, "").replace(self.base_uri, "../")
for c in content]
uri = uuid.uuid4().urn
ann = {
"uri": uri,
"abou... | def add_annotation(self, about, content, motivated_by="oa:describing") | Cheap URI relativize for current directory and /. | 4.299294 | 4.129321 | 1.041163 |
# type: (MutableMapping[Text, Any]) -> None
self.self_check()
for key, value in prov_dep.items():
if key == "location" and value.split("/")[-1]:
filename = value.split("/")[-1]
path = os.path.join(self.folder, SNAPSHOT, filename)
... | def generate_snapshot(self, prov_dep) | Copy all of the CWL files to the snapshot/ directory. | 4.072756 | 3.715724 | 1.096087 |
# YAML is always UTF8, but json.dumps gives us str in py2
write_pack.write(packed.encode(ENCODING))
_logger.debug(u"[provenance] Added packed workflow: %s", rel_path) | def packed_workflow(self, packed): # type: (Text) -> None
self.self_check()
rel_path = posixpath.join(_posix_path(WORKFLOW), "packed.cwl")
# Write as binary
with self.write_bag_file(rel_path, encoding=None) as write_pack | Pack CWL description to generate re-runnable CWL object in RO. | 11.485443 | 13.286945 | 0.864416 |
def has_data_file(self, sha1hash): # type: (str) -> bool
folder = os.path.join(self.folder, DATA, sha1hash[0:2])
hash_path = os.path.join(folder, sha1hash)
return os.path.isfile(hash_path) | Confirms the presence of the given file in the RO. | null | null | null | |
# type: (IO, Optional[datetime.datetime], Optional[str]) -> Text
self.self_check()
tmp_dir, tmp_prefix = os.path.split(self.temp_prefix)
with tempfile.NamedTemporaryFile(
prefix=tmp_prefix, dir=tmp_dir, delete=False) as tmp:
checksum = checksum_copy(f... | def add_data_file(self, from_fp, timestamp=None, content_type=None) | Copy inputs to data/ folder. | 4.539057 | 4.535145 | 1.000863 |
# type: (Text, Dict[str,str]) -> None
self.self_check()
if posixpath.isabs(rel_path):
raise ValueError("rel_path must be relative: %s" % rel_path)
if posixpath.commonprefix(["data/", rel_path]) == "data/":
# payload file, go to manifest
manif... | def add_to_manifest(self, rel_path, checksums) | Add files to the research object manifest. | 5.800461 | 5.762374 | 1.00661 |
return dict(o)
if is_output:
rel_path = posixpath.join(_posix_path(WORKFLOW), "primary-output.json")
else:
rel_path = posixpath.join(_posix_path(WORKFLOW), "primary-job.json")
j = json_dumps(copied, indent=4, ensure_ascii=False, default=jdefault)
with ... | def create_job(self,
builder_job, # type: Dict[Text, Any]
wf_job=None, # type: Callable[[Dict[Text, Text], Callable[[Any, Any], Any], RuntimeContext], Generator[Any, None, None]]
is_output=False
): # type: (...) -> Dict
#TODO cust... | Generate the new job object with RO specific relative paths. | 3.609265 | 3.550532 | 1.016542 |
# type: (Dict[Any, Any]) -> None
# Base case - we found a File we need to update
_logger.debug(u"[provenance] Relativising: %s", structure)
if isinstance(structure, MutableMapping):
if structure.get("class") == "File":
relative_path = None
... | def _relativise_files(self, structure) | Save any file objects into the RO and update the local paths. | 5.240483 | 5.105295 | 1.02648 |
# type: (Optional[str]) -> None
if save_to is None:
if not self.closed:
_logger.debug(u"[provenance] Deleting temporary %s", self.folder)
shutil.rmtree(self.folder, ignore_errors=True)
else:
save_to = os.path.abspath(save_to)
... | def close(self, save_to=None) | Close the Research Object, optionally saving to specified folder.
Closing will remove any temporary files used by this research object.
After calling this method, this ResearchObject instance can no longer
be used, except for no-op calls to .close().
The 'saveTo' folder should not exis... | 3.196455 | 3.203749 | 0.997723 |
return u""
return rdf.decode('utf-8') | def printrdf(wflow, ctx, style): # type: (Process, ContextType, Text) -> Text
rdf = gather(wflow, ctx).serialize(format=style, encoding='utf-8')
if not rdf | Serialize the CWL document into a string, ready for printing. | 11.778735 | 11.011937 | 1.069633 |
# type: (...) -> bool
found = False
candidates = []
if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
match = re.search(pattern=r'([a-z]*://)', string=dockerRequirement["dockerPull"])
candidate = _normalize_image_id(dock... | def get_image(dockerRequirement, # type: Dict[Text, Text]
pull_image, # type: bool
force_pull=False # type: bool
) | Acquire the software container image in the specified dockerRequirement
using Singularity and returns the success as a bool. Updates the
provided dockerRequirement with the specific dockerImageId to the full
path of the local image, if found. Likewise the
dockerRequirement['dockerPull'] ... | 2.567498 | 2.513749 | 1.021382 |
# type: (...) -> Optional[Text]
if not bool(spawn.find_executable('singularity')):
raise WorkflowException('singularity executable is not available')
if not self.get_image(r, pull_image, force_pull):
raise WorkflowException(u"Container image {} not "
... | def get_from_requirements(self,
r, # type: Dict[Text, Text]
pull_image, # type: bool
force_pull=False, # type: bool
tmp_outdir_prefix=None # type: Text
... | Returns the filename of the Singularity image (e.g.
hello-world-latest.img). | 4.911213 | 4.932778 | 0.995628 |
runtime.append(u"--userns")
runtime.append(u"--bind")
runtime.append(u"{}:{}:rw".format(
docker_windows_path_adjust(os.path.realpath(self.outdir)),
self.builder.outdir))
runtime.append(u"--bind")
tmpdir = "/tmp" # nosec
runtime.append(u"{}:{}:... | def create_runtime(self,
env, # type: MutableMapping[Text, Text]
runtime_context # type: RuntimeContext
): # type: (...) -> Tuple[List, Optional[Text]]
any_path_okay = self.builder.get_requirement("DockerRequirement")[1] \... | Returns the Singularity runtime list of commands and options. | 2.839666 | 2.730239 | 1.040079 |
result = subprocess.check_output(cmd, stderr=subprocess.STDOUT)
return result.strip()
except (OSError, subprocess.CalledProcessError, TypeError, AttributeError):
# OSError is raised if command doesn't exist
# CalledProcessError is raised if command returns nonzero
# Attribute... | def check_output_and_strip(cmd): # type: (List[Text]) -> Optional[Text]
try | Passes a command list to subprocess.check_output, returning None
if an expected exception is raised
:param cmd: The command to execute
:return: Stripped string output of the command, or None if error | 4.441829 | 4.557132 | 0.974698 |
return (None, None)
uid = cmd_output_to_int(['docker-machine', 'ssh', machine_name, "id -u"])
gid = cmd_output_to_int(['docker-machine', 'ssh', machine_name, "id -g"])
return (uid, gid) | def docker_machine_id(): # type: () -> Tuple[Optional[int], Optional[int]]
machine_name = docker_machine_name()
if not machine_name | Asks docker-machine for active machine and gets the UID of the docker user
inside the vm
:return: tuple (UID, GID), or (None, None) if error (e.g. docker-machine not present or stopped) | 3.074366 | 2.992671 | 1.027298 |
loadingContext = LoadingContext()
loadingContext.loader = default_loader()
else:
loadingContext = loadingContext.copy()
if loadingContext.loader is None:
loadingContext.loader = default_loader(loadingContext.fetcher_constructor)
if isinstance(argsworkflow, string_typ... | def fetch_document(argsworkflow, # type: Union[Text, Dict[Text, Any]]
loadingContext=None # type: Optional[LoadingContext]
): # type: (...) -> Tuple[LoadingContext, CommentedMap, Text]
if loadingContext is None | Retrieve a CWL document. | 4.308359 | 3.667494 | 1.174742 |
raise ValueError("loadingContext must have a loader")
resolveduri, metadata = loadingContext.loader.resolve_ref(uri)
processobj = None
if isinstance(resolveduri, MutableSequence):
for obj in resolveduri:
if obj['id'].endswith('#main'):
processobj = obj
... | def make_tool(uri, # type: Union[Text, CommentedMap, CommentedSeq]
loadingContext # type: LoadingContext
): # type: (...) -> Process
if loadingContext.loader is None | Make a Python CWL object. | 4.578979 | 4.253862 | 1.076429 |
# type: (Builder, Text, Dict[Text, Any]) -> Union[Dict[Text, Any], None]
split = urllib.parse.urlsplit(outdir)
if not split.scheme:
outdir = file_uri(str(outdir))
# builder.outdir is the inner (container/compute node) output directory
# outdir is the outer (host/storage system) outpu... | def revmap_file(builder, outdir, f) | Remap a file from internal path to external path.
For Docker, this maps from the path inside tho container to the path
outside the container. Recognizes files in the pathmapper or remaps
internal output directories to the external directory. | 4.125576 | 4.11211 | 1.003275 |
# type: (Builder, Dict[Text, Any]) -> Dict[Text, Any]
if not builder.pathmapper:
raise ValueError("Do not call check_adjust using a builder that doesn't have a pathmapper.")
file_o["path"] = docker_windows_path_adjust(
builder.pathmapper.mapper(file_o["location"])[1])
dn, bn = ... | def check_adjust(builder, file_o) | Map files to assigned path inside a container.
We need to also explicitly walk over input, as implicit reassignment
doesn't reach everything in builder.bindings | 3.320813 | 3.398672 | 0.977091 |
sjob = copy.copy(joborder)
sjob[scatter_key] = joborder[scatter_key][index]
if len(scatter_keys) == 1:
if runtimeContext.postScatterEval is not None:
sjob = runtimeContext.postScatterEval(sjob)
steps.append(process.job(
sjob, functools.par... | def _flat_crossproduct_scatter(process, # type: WorkflowJobStep
joborder, # type: MutableMapping[Text, Any]
scatter_keys, # type: MutableSequence[Text]
callback, # type: ReceiveScatterOutput
... | Inner loop. | 2.885459 | 2.810412 | 1.026703 |
# type: (Text, Text, Optional[Graph], Set[Text]) -> bool
if URIRef(fmt) == URIRef(cls):
return True
if ontology is None:
return False
if fmt in visited:
return False
visited.add(fmt)
uriRefFmt = URIRef(fmt)
for s, p, o in ontology.triples((uriRefFmt, RDFS.s... | def formatSubclassOf(fmt, cls, ontology, visited) | Determine if `fmt` is a subclass of `cls`. | 2.223917 | 2.104188 | 1.0569 |
if not afile:
continue
if "format" not in afile:
raise validate.ValidationException(
u"File has no 'format' defined: {}".format(
json_dumps(afile, indent=4)))
for inpf in aslist(input_formats):
if afile["format"] == inpf or ... | def check_format(actual_file, # type: Union[Dict[Text, Any], List, Text]
input_formats, # type: Union[List[Text], Text]
ontology # type: Optional[Graph]
): # type: (...) -> None
for afile in aslist(actual_file) | Confirms that the format present is valid for the allowed formats. | 3.975965 | 3.696781 | 1.075521 |
if "requirements" in t:
for r in t["requirements"]:
if r["class"] in rewrite:
r["class"] = rewrite[r["class"]]
if "hints" in t:
for r in t["hints"]:
if r["class"] in rewrite:
r["class"] = rewrite[r["class"]]
... | def v1_0to1_1_0dev1(doc, loader, baseuri): # pylint: disable=unused-argument
# type: (Any, Loader, Text) -> Tuple[Any, Text]
doc = copy.deepcopy(doc)
rewrite = {
"http://commonwl.org/cwltool#WorkReuse": "WorkReuse",
"http://commonwl.org/cwltool#TimeLimit": "ToolTimeLimit",
"h... | Public updater for v1.0 to v1.1.0-dev1. | 2.862266 | 2.741783 | 1.043943 |
# type: (...) -> Tuple[Union[CommentedSeq, CommentedMap], Text]
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... | def checkversion(doc, # type: Union[CommentedSeq, CommentedMap]
metadata, # type: CommentedMap
enable_dev # type: bool
) | Checks the validity of the version of the give CWL document.
Returns the document and the validated version string. | 3.204713 | 3.150372 | 1.017249 |
# type: (str) -> bool
# parse nodejs version into int Tuple: 'v4.2.6\n' -> [4, 2, 6]
current_version_str = subprocess.check_output(
[working_alias, "-v"]).decode('utf-8')
current_version = [int(v) for v in current_version_str.strip().strip('v').split('.')]
minimum_node_version = [int(... | def check_js_threshold_version(working_alias) | Checks if the nodeJS engine version on the system
with the allowed minimum version.
https://github.com/nodejs/node/blob/master/CHANGELOG.md#nodejs-changelog | 3.625526 | 4.127 | 0.878489 |
if not entry.staged:
continue
if not os.path.exists(os.path.dirname(entry.target)):
os.makedirs(os.path.dirname(entry.target))
if entry.type in ("File", "Directory") and os.path.exists(entry.resolved):
if symlink: # Use symlink func if allowed
... | def stage_files(pathmapper, # type: PathMapper
stage_func=None, # type: Callable[..., Any]
ignore_writable=False, # type: bool
symlink=True, # type: bool
secret_store=None # type: SecretStore
): # type: (... | Link or copy files to their targets. Create them as needed. | 2.235059 | 2.194058 | 1.018687 |
# type: (Union[List[Dict[Text, Any]], Dict[Text, Any]], Text) -> Any
if isinstance(field_type, MutableSequence):
for field in field_type:
avroize_type(field, name_prefix)
elif isinstance(field_type, MutableMapping):
if field_type["type"] in ("enum", "record"):
if... | def avroize_type(field_type, name_prefix="") | adds missing information to a type so that CWL types are valid in schema_salad. | 1.974519 | 1.901908 | 1.038178 |
if "var/spool/cwl" in obj and obj_key != "dockerOutputDirectory":
_logger.warning(
SourceLine(item=item, key=obj_key, raise_type=Text).makeError(
_VAR_SPOOL_ERROR.format(obj)))
r = True
elif isinstance(obj, MutableMapping):
for key, value i... | def var_spool_cwl_detector(obj, # type: Union[MutableMapping, List, Text]
item=None, # type: Optional[Any]
obj_key=None, # type: Optional[Any]
): # type: (...)->bool
r = False
if isinstance(obj, stri... | Detects any textual reference to /var/spool/cwl. | 3.837018 | 3.335389 | 1.150396 |
# type: () -> Text
'''
version of CWLtool used to execute the workflow.
'''
pkg = pkg_resources.require("cwltool")
if pkg:
return u"%s %s" % (sys.argv[0], pkg[0].version)
return u"%s %s" % (sys.argv[0], "unknown version") | def versionstring() | version of CWLtool used to execute the workflow. | 3.848652 | 3.196059 | 1.204187 |
# type: (Text) -> Text
r
if onWindows():
split = path.split(':')
if len(split) == 2:
if platform.win32_ver()[0] in ('7', '8'): # type: ignore
split[0] = split[0].lower() # Docker toolbox uses lowecase windows Drive letters
else:
split... | def docker_windows_path_adjust(path) | r"""
Changes only windows paths so that the can be appropriately passed to the
docker run command as as docker treats them as unix paths.
Example: 'C:\Users\foo to /C/Users/foo (Docker for Windows) or /c/Users/foo
(Docker toolbox). | 4.482332 | 4.555577 | 0.983922 |
# type: (Text) -> (Text)
r
if path is not None and onWindows():
if path[0] == '/':
path = path[1:]
else:
raise ValueError("not a docker path")
splitpath = path.split('/')
splitpath[0] = splitpath[0]+':'
return '\\'.join(splitpath)
return pa... | def docker_windows_reverse_path_adjust(path) | r"""
Change docker path (only on windows os) appropriately back to Window path/
Example: /C/Users/foo to C:\Users\foo | 4.48825 | 5.094244 | 0.881043 |
# type: (Text) -> (Text)
r
if fileuri is not None and onWindows():
if urllib.parse.urlsplit(fileuri).scheme == "file":
filesplit = fileuri.split("/")
if filesplit[3][-1] != ':':
filesplit[3] = filesplit[3]+':'
return '/'.join(filesplit)
... | def docker_windows_reverse_fileuri_adjust(fileuri) | r"""
On docker in windows fileuri do not contain : in path
To convert this file uri to windows compatible add : after drive letter,
so file:///E/var becomes file:///E:/var | 4.344378 | 5.174297 | 0.839607 |
if i == j:
continue
# in case 1st list is smaller
# should come first in sorting
if i is None:
return -1
# if 1st list is longer,
# it should come later in sort
elif j is None:
return 1
# if either of the list contains ... | def cmp_like_py2(dict1, dict2): # type: (Dict[Text, Any], Dict[Text, Any]) -> int
# extract lists from both dicts
first, second = dict1["position"], dict2["position"]
# iterate through both list till max of their size
for i, j in zip_longest(first, second) | Comparision function to be used in sorting as python3 doesn't allow sorting
of different types like str() and int().
This function re-creates sorting nature in py2 of heterogeneous list of
`int` and `str` | 4.269977 | 4.496028 | 0.949722 |
# type: (...) -> Union[Text, MutableSequence[Any], MutableMapping[Text, Any]]
# if input is dict, recursively call for each value
if isinstance(inp, MutableMapping):
for k in inp:
inp[k] = bytes2str_in_dicts(inp[k])
return inp
# if list, iterate through list and fn cal... | def bytes2str_in_dicts(inp # type: Union[MutableMapping[Text, Any], MutableSequence[Any], Any]
) | Convert any present byte string to unicode string, inplace.
input is a dict of nested dicts and lists | 3.134932 | 3.32799 | 0.94199 |
# type: (Any, Iterable, Union[Callable[..., Any], partial[Any]]) -> None
if isinstance(rec, MutableMapping):
if "class" in rec and rec.get("class") in cls:
op(rec)
for d in rec:
visit_class(rec[d], cls, op)
if isinstance(rec, MutableSequence):
for d in r... | def visit_class(rec, cls, op) | Apply a function to with "class" in cls. | 3.600389 | 3.654803 | 0.985112 |
# type: (Any, Iterable, Union[Callable[..., Any], partial[Any]]) -> None
if isinstance(rec, MutableMapping):
if field in rec:
rec[field] = op(rec[field])
for d in rec:
visit_field(rec[d], field, op)
if isinstance(rec, MutableSequence):
for d in rec:
... | def visit_field(rec, field, op) | Apply a function to mapping with 'field'. | 3.108854 | 3.058803 | 1.016363 |
random_outdir.outdir = '/' + ''.join([random.choice(string.ascii_letters) for _ in range(6)]) # type: ignore # nosec
return random_outdir.outdir | def random_outdir(): # type: () -> Text
# compute this once and store it as a function attribute - each subsequent call will return the same value
if not hasattr(random_outdir, 'outdir') | Return the random directory name chosen to use for tool / workflow output | 3.825633 | 3.441645 | 1.111571 |
''' Write a numeric result in various forms '''
out('hex: 0x{0:08x}'.format(num))
out('dec: {0:d}'.format(num))
out('oct: 0o{0:011o}'.format(num))
out('bin: 0b{0:032b}'.format(num)) | def print_num(num) | Write a numeric result in various forms | 3.70055 | 3.107255 | 1.190939 |
''' Runs the program and handles command line options '''
parser = get_parser()
# Parse arguments and run the function
global args
args = parser.parse_args(argv)
args.func() | def main(argv=None) | Runs the program and handles command line options | 6.649134 | 5.455354 | 1.218827 |
if getattr(self, fieldname): # do not overwrite existing data
return
value = bytestring if transfunc is None else transfunc(bytestring)
if DEBUG:
stderr('Setting field "%s" to "%s"' % (fieldname, value))
if fieldname == 'genre' and value.isdigit() and in... | def _set_field(self, fieldname, bytestring, transfunc=None) | convienience function to set fields of the tinytag by name.
the payload (bytestring) can be changed using the transfunc | 3.63879 | 3.655301 | 0.995483 |
if value_type == 0: # Unicode string
return self.__decode_string(value)
elif value_type == 1: # BYTE array
return value
elif 1 < value_type < 6: # DWORD / QWORD / WORD
return _bytes_to_int_le(value) | def __decode_ext_desc(self, value_type, value) | decode ASF_EXTENDED_CONTENT_DESCRIPTION_OBJECT values | 4.773566 | 4.339852 | 1.099937 |
return super(Card, self).fetch(card_id, data, **kwargs) | def fetch(self, card_id, data={}, **kwargs) | Fetch Card for given Id
Args:
card_id : Id for which card object has to be retrieved
Returns:
Card dict for given card Id | 3.783141 | 7.08352 | 0.534076 |
return super(VirtualAccount, self).all(data, **kwargs) | def all(self, data={}, **kwargs) | Fetch all Virtual Account entities
Returns:
Dictionary of Virtual Account data | 9.277731 | 7.078048 | 1.310775 |
return super(VirtualAccount, self).fetch(
virtual_account_id,
data,
**kwargs) | def fetch(self, virtual_account_id, data={}, **kwargs) | Fetch Virtual Account for given Id
Args:
virtual_account_id :
Id for which Virtual Account object has to be retrieved
Returns:
Virtual Account dict for given Virtual Account Id | 3.675697 | 5.865595 | 0.626654 |
url = self.base_url
return self.post_url(url, data, **kwargs) | def create(self, data={}, **kwargs) | Create Virtual Account from given dict
Args:
Param for Creating Virtual Account
Returns:
Virtual Account dict | 5.067487 | 8.674877 | 0.584157 |
url = "{}/{}".format(self.base_url, virtual_account_id)
data['status'] = 'closed'
return self.patch_url(url, data, **kwargs) | def close(self, virtual_account_id, data={}, **kwargs) | Close Virtual Account from given Id
Args:
virtual_account_id :
Id for which Virtual Account objects has to be Closed | 3.299013 | 4.01466 | 0.821741 |
url = "{}/{}/payments".format(self.base_url, virtual_account_id)
return self.get_url(url, data, **kwargs) | def payments(self, virtual_account_id, data={}, **kwargs) | Fetch Payment for Virtual Account Id
Args:
virtual_account_id :
Id for which Virtual Account objects has to be retrieved
Returns:
Payment dict for given Virtual Account Id | 2.932149 | 3.794897 | 0.772656 |
return super(Subscription, self).all(data, **kwargs) | def all(self, data={}, **kwargs) | Fetch all Subscription entities
Returns:
Dictionary of Subscription data | 7.566944 | 7.476111 | 1.01215 |
return super(Subscription, self).fetch(subscription_id, data, **kwargs) | def fetch(self, subscription_id, data={}, **kwargs) | Fetch Subscription for given Id
Args:
subscription_id : Id for which subscription object is retrieved
Returns:
Subscription dict for given subscription Id | 3.63751 | 6.65626 | 0.54648 |
url = "{}/{}/cancel".format(self.base_url, subscription_id)
return self.post_url(url, data, **kwargs) | def cancel(self, subscription_id, data={}, **kwargs) | Cancel subscription given by subscription_id
Args:
subscription_id : Id for which subscription has to be cancelled
Returns:
Subscription Dict for given subscription id | 3.172784 | 4.322258 | 0.734057 |
return super(Order, self).all(data, **kwargs) | def all(self, data={}, **kwargs) | Fetch all Order entities
Returns:
Dictionary of Order data | 6.943742 | 7.85114 | 0.884425 |
return super(Order, self).fetch(order_id, data, **kwargs) | def fetch(self, order_id, data={}, **kwargs) | Fetch Order for given Id
Args:
order_id : Id for which order object has to be retrieved
Returns:
Order dict for given order Id | 3.568805 | 7.224421 | 0.493992 |
return super(Customer, self).fetch(customer_id, data, **kwargs) | def fetch(self, customer_id, data={}, **kwargs) | Fetch Customer for given Id
Args:
customer_id : Id for which customer object has to be retrieved
Returns:
Order dict for given customer Id | 3.513194 | 6.588949 | 0.533195 |
url = '{}/{}'.format(self.base_url, customer_id)
return self.put_url(url, data, **kwargs) | def edit(self, customer_id, data={}, **kwargs) | Edit Customer information from given dict
Returns:
Customer Dict which was edited | 3.434455 | 5.361854 | 0.640535 |
return super(Addon, self).fetch(addon_id, data, **kwargs) | def fetch(self, addon_id, data={}, **kwargs) | Fetch addon for given Id
Args:
addon_id : Id for which addon object has to be retrieved
Returns:
addon dict for given subscription Id | 3.371734 | 7.271015 | 0.463723 |
return super(Addon, self).delete(addon_id, data, **kwargs) | def delete(self, addon_id, data={}, **kwargs) | Delete addon for given id
Args:
addon_id : Id for which addon object has to be deleted | 3.23023 | 6.589307 | 0.490223 |
return super(Refund, self).all(data, **kwargs) | def all(self, data={}, **kwargs) | Fetch All Refund
Returns:
Refund dict | 9.180164 | 8.324315 | 1.102813 |
return super(Refund, self).fetch(refund_id, data, **kwargs) | def fetch(self, refund_id, data={}, **kwargs) | Refund object for given paymnet Id
Args:
refund_id : Refund Id for which refund has to be retrieved
Returns:
Refund dict for given refund Id | 3.456102 | 6.80172 | 0.508122 |
return super(Payment, self).all(data, **kwargs) | def all(self, data={}, **kwargs) | Fetch all Payment entities
Returns:
Dictionary of Payment data | 7.493647 | 7.619921 | 0.983428 |
return super(Payment, self).fetch(payment_id, data, **kwargs) | def fetch(self, payment_id, data={}, **kwargs) | Fetch Payment for given Id
Args:
payment_id : Id for which payment object has to be retrieved
Returns:
Payment dict for given payment Id | 3.618662 | 6.810153 | 0.531363 |
url = "{}/{}/capture".format(self.base_url, payment_id)
data['amount'] = amount
return self.post_url(url, data, **kwargs) | def capture(self, payment_id, amount, data={}, **kwargs) | Capture Payment for given Id
Args:
payment_id : Id for which payment object has to be retrieved
Amount : Amount for which the payment has to be retrieved
Returns:
Payment dict after getting captured | 2.987216 | 4.559299 | 0.655192 |
url = "{}/{}/transfers".format(self.base_url, payment_id)
return self.post_url(url, data, **kwargs) | def transfer(self, payment_id, data={}, **kwargs) | Create Transfer for given Payment Id
Args:
payment_id : Id for which payment object has to be transfered
Returns:
Payment dict after getting transfered | 3.081543 | 5.137264 | 0.599841 |
url = "{}/{}/transfers".format(self.base_url, payment_id)
return self.get_url(url, data, **kwargs) | def transfers(self, payment_id, data={}, **kwargs) | Fetches all transfer for given Payment Id
Args:
payment_id : Id for which payment object has to be refunded
Amount : Amount for which the payment has to be refunded
Returns:
Payment dict after getting refunded | 2.981315 | 4.988217 | 0.597671 |
return super(Plan, self).fetch(plan_id, data, **kwargs) | def fetch(self, plan_id, data={}, **kwargs) | Fetch Plan for given Id
Args:
plan_id : Id for which Plan object has to be retrieved
Returns:
Plan dict for given subscription Id | 3.632527 | 7.1589 | 0.507414 |
return super(Plan, self).all(data, **kwargs) | def all(self, data={}, **kwargs) | Fetch all plan entities
Returns:
Dictionary of plan data | 8.12765 | 8.584905 | 0.946737 |
url = "{}/{}/tokens/{}".format(self.base_url, customer_id, token_id)
return self.get_url(url, data, **kwargs) | def fetch(self, customer_id, token_id, data={}, **kwargs) | Fetch Token for given Id and given customer Id
Args:
customer_id : Customer Id for which tokens have to be fetched
token_id : Id for which TOken object has to be fetched
Returns:
Token dict for given token Id | 2.755684 | 4.005899 | 0.687907 |
url = "{}/{}/tokens".format(self.base_url, customer_id)
return self.get_url(url, data, **kwargs) | def all(self, customer_id, data={}, **kwargs) | Get all tokens for given customer Id
Args:
customer_id : Customer Id for which tokens have to be fetched
Returns:
Token dicts for given cutomer Id | 4.036983 | 4.194809 | 0.962376 |
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