def dump(references: List[Dict], file: TextIO, mapping: Optional[Dict] = None):
"""Write an RIS file to file or file-like object.
Entries are codified as dictionaries whose keys are the
different tags. For single line and singly occurring tags,
the content is codified as a string. In the case of multiline
or multiple key occurrences, the content is returned as a list
of strings.
Args:
references (List[Dict]): List of references.
file (TextIO): File handle to store ris formatted data.
mapping (Dict, optional): Custom RIS tags mapping.
"""
text = dumps(references, mapping)
file.writelines(text)
async def cli_main(
config: confuse.Configuration,
*,
input: TextIO,
output: TextIO,
include_unparsed: bool,
) -> None:
async def _yield_input() -> AsyncIterable[git.Commit]:
for line in input:
item = json.loads(line)
yield item
stream = main(config,
input=_yield_input(),
include_unparsed=include_unparsed)
async for item in stream:
line = json.dumps(item, default=json_defaults)
output.writelines([line, "\n"])
def _generate_template_to_writer(self, base: pathlib.Path,
source: pathlib.Path, writer: TextIO,
**extra_variables):
try:
template = self.env.get_template(str(source))
except jinja2.TemplateNotFound as e:
raise GeneratorError(
"Template {} not found (search path {})".format(
source, self._format_search_path())) from e
now = datetime.datetime.now(datetime.timezone.utc).astimezone()
comment = ("Generated on {} from {} by {}".format(
now.strftime(self.DATETIME_FORMAT), source, self._current_user))
relative_source = source.relative_to(base)
stream = template.stream(**self.config,
**extra_variables,
comment=comment,
source_base=base,
source=relative_source,
source_dir=relative_source.parent)
writer.writelines(stream)
def print_config(verbose: bool = False, stream: TextIO = None) -> None:
from pathlib import Path
if stream is None:
stream = sys.stdout
stream.writelines([
f"ezdxf {__version__} from {Path(__file__).parent}\n",
f"Python version: {sys.version}\n",
f"using C-extensions: {YES_NO[options.use_c_ext]}\n",
f"using Matplotlib: {YES_NO[options.use_matplotlib]}\n",
])
if verbose:
stream.write("\nConfiguration:\n")
options.write(stream)
stream.write("\nEnvironment Variables:\n")
for v in options.CONFIG_VARS:
stream.write(f"{v}={os.environ.get(v, '')}\n")
stream.write("\nLoaded Config Files:\n")
for path in options.loaded_config_files:
stream.write(str(path.absolute()) + "\n")
def try_to_write_header_to_output_file(
self,
project_or_project_and_group: str,
output_file: TextIO,
empty_config: bool = False,
):
"""
Writes a shared key for the "_write_to_file" method which actually dumps the configurations.
"""
if output_file:
try:
if empty_config:
output_file.writelines(
f"{project_or_project_and_group}: {{}}\n")
else:
output_file.writelines(
f"{project_or_project_and_group}:\n")
except Exception as e:
logging.error(
f"Error when trying to write to {output_file.name}: {e}")
raise e
def _generate_template_to_writer(self, base: pathlib.Path,
source: pathlib.Path,
writer: TextIO, **extra_variables):
try:
template = self.env.get_template(str(source))
except jinja2.TemplateNotFound as e:
raise GeneratorError("Template {} not found (search path {})"
.format(source,
self._format_search_path())
) from e
now = datetime.datetime.now(datetime.timezone.utc).astimezone()
comment = ("Generated on {} from {} by {}"
.format(now.strftime(self.DATETIME_FORMAT), source,
self._current_user))
relative_source = source.relative_to(base)
stream = template.stream(**self.config, **extra_variables,
comment=comment,
source_base=base,
source=relative_source,
source_dir=relative_source.parent)
writer.writelines(stream)
def _write_table(
module_name: str,
module_path: str,
supported_status: Dict[str, SupportedStatus],
w_fd: TextIO,
) -> None:
"""
Write table by using Sphinx list-table directive.
"""
lines = []
lines.append("Supported ")
if module_name:
lines.append(module_name)
else:
lines.append("General Function")
lines.append(" APIs\n")
lines.append("-" * 100)
lines.append("\n")
lines.append(".. currentmodule:: %s" % module_path)
if module_name:
lines.append(".%s\n" % module_name)
else:
lines.append("\n")
lines.append("\n")
lines.append(".. list-table::\n")
lines.append(" :header-rows: 1\n")
lines.append("\n")
lines.append(" * - API\n")
lines.append(" - Implemented\n")
lines.append(" - Missing parameters\n")
for func_str, status in supported_status.items():
func_str = _escape_func_str(func_str)
if status.implemented == Implemented.NOT_IMPLEMENTED.value:
lines.append(" * - %s\n" % func_str)
else:
lines.append(" * - :func:`%s`\n" % func_str)
lines.append(" - %s\n" % status.implemented)
lines.append(" - \n") if not status.missing else lines.append(
" - %s\n" % status.missing)
w_fd.writelines(lines)
def _write_to_file(
self,
configuration_to_process,
output_file: TextIO,
):
"""
Writes indented content of a dict under a key from "try_to_write_header_to_output_file" method.
"""
try:
output_file.writelines(f" {self.__configuration_name}:\n", )
indented_configuration = textwrap.indent(
yaml.dump(
configuration_to_process,
default_flow_style=False,
),
" ",
)
output_file.write(indented_configuration)
except Exception as e:
logging.error(
f"Error when trying to write to {output_file.name}: {e}")
raise e
def write_default_config(self, cfg_file: TextIO) -> None:
"""Write default configuration for all known tasks into file.
Arguments:
:cfg_file: Openned file-like object.
"""
# Write list of tasks
cfg_file.write("""; ---------------------------
; Task executor configuration
; ---------------------------
""")
for option in self.config.options.values():
cfg_file.writelines(option.get_config())
cfg_file.write("\n")
#
seen_options = {}
multi_used = {}
# collect all options from tasks
for task in self.tasks:
for name in task.config.options:
seen_options.setdefault(name, list()).append(task.name)
# Options used by multiple tasks
for name, tasks in seen_options.items():
if len(tasks) > 1:
multi_used[name] = tasks
cfg_file.write("; ------------------------------\n")
cfg_file.write("; Options used by multiple tasks\n")
cfg_file.write("; ------------------------------\n\n")
for name, tasks in multi_used.items():
task = self.get_task(tasks[0])
option = task.config.get_option(name)
lines = option.get_config()
lines.insert(
len(lines) - 1, "; Used by tasks: %s\n" % ', '.join(tasks))
lines.insert(len(lines) - 1, ";\n")
cfg_file.writelines(lines)
cfg_file.write("\n")
# Options used by only one task
for task in self.tasks:
title = "Task '%s'" % task.name
cfg_file.write("; %s\n" % ('-' * len(title)))
cfg_file.write("; %s\n" % title)
cfg_file.write("; %s\n\n" % ('-' * len(title)))
has_options = False
for name, option in task.config.options.items():
if name not in multi_used:
has_options = True
cfg_file.writelines(option.get_config())
cfg_file.write("\n")
if not has_options:
if task.config.options:
cfg_file.write(
"; This task has no private options (not shared with other tasks).\n"
)
else:
cfg_file.write(
"; This task has no configuration options.\n")
cfg_file.write("\n")
def dump(
references: List[Dict],
file: TextIO,
*,
implementation: Optional[BaseWriter] = None,
**kw,
):
"""Write an RIS file to file or file-like object.
Entries are codified as dictionaries whose keys are the
different tags. For single line and singly occurring tags,
the content is codified as a string. In the case of multiline
or multiple key occurrences, the content is returned as a list
of strings.
Args:
references (List[Dict]): List of references.
file (TextIO): File handle to store ris formatted data.
implementation (RisImplementation): RIS implementation; base by
default.
"""
text = dumps(references, implementation=implementation, **kw)
file.writelines(text)
def write(file: TextIO, fields: List[str]) -> Generator:
"""
the writer method for tab format
"""
if 'seqid' not in fields:
raise ValueError("Tab format expects a 'seqid'")
# write the heading
file.write('\t'.join(fields) + '\n')
while True:
# receive a record
try:
record = yield
except GeneratorExit:
break
# enforce name uniqueness
unicifier = Unicifier()
record['seqid'] = unicifier.unique(record['seqid'])
# collect record fields in a list and join them with tabs
file.writelines('\t'.join([record[field]
for field in fields]) + '\n')
def dump(
file: TextIO,
scenario_paths: Iterable[LaxPath],
plugins: Sequence[PluginName] = (),
with_default_plugins: bool = True,
) -> None:
"""
Transforms the provided *scenario_paths* using the provided *plugins*,
and writes the resulting locustfile code in the provided *file*.
See also: :func:`dumps`
:param file: an object with a `writelines` method (as specified by
io.TextIOBase), e.g. `sys.stdout` or the result of `open`.
:param scenario_paths: paths to scenario files (HAR) or directories.
:param plugins: names of plugins to use.
:param with_default_plugins: whether the default plugins should be used in
addition to those provided (recommended: True).
"""
file.writelines(
intersperse(
"\n", _dump_as_lines(scenario_paths, plugins,
with_default_plugins)))
def dump(obj: List[ButtonBatchLine], fp: TextIO):
fp.writelines([x.line for x in obj])
def write_to(self, output: TextIO):
if self._as_file_path is not None:
with self._as_file_path.open() as f_cached:
output.writelines(f_cached)
else:
self._writer.write(self._tmp_file_space, output)
def _write_lines(file: TextIO, lines):
file.writelines((str(i) + "\n" for i in lines))
def sample_export(results, file_handle: TextIO):
"""
Renders Biosamples as a clinical_sample text file suitable for
importing by cBioPortal.
cBioPortal Sample fields specs:
---------------------------------
Required:
- PATIENT_ID
- SAMPLE_ID
Special columns:
- For pan-cancer summary statistics tab:
- CANCER_TYPE as an Oncotree code
- CANCER_TYPE_DETAILED
- SAMPLE_DISPLAY_NAME
- SAMPLE_CLASS
- METASTATIC_SITE / PRIMARY_SITE overrides the patients level attribute TUMOR_SITE
- SAMPLE_TYPE, TUMOR_TISSUE_SITE, TUMOR_TYPE can have the following values
(are displayed with a distinct color in the timelines):
- "recurrence", "recurred", "progression"
- "metastatic", "metastasis"
- "primary" or any other value
- KNOWN_MOLECULAR_CLASSIFIER
- GLEASON_SCORE (prostate cancer)
- HISTOLOGY
- TUMOR_STAGE_2009
- TUMOR_GRADE
- ETS_RAF_SPINK1_STATUS
- TMPRSS2_ERG_FUSION_STATUS
- ERG_FUSION_ACGH
- SERUM_PSA
- DRIVER_MUTATIONS
"""
samples = []
for sample in results:
# sample.inidividual may be null: use Phenopacket model Subject field
# instead if available or skip.
subject_id = None
if sample.individual is not None:
subject_id = sample.individual
elif sample.phenopacket_subject_id is not None:
subject_id = sample.phenopacket_subject_id
else:
continue
sample_obj = {
'individual_id': subject_id,
'id': sample.id
}
if sample.sampled_tissue:
sample_obj['tissue_label'] = sample.sampled_tissue.get('label', '')
samples.append(sample_obj)
columns = samples[0].keys()
headers = biosample_to_sample_header(columns)
file_handle.writelines([line + '\n' for line in headers])
dict_writer = csv.DictWriter(file_handle, fieldnames=columns, delimiter='\t')
dict_writer.writerows(samples)
def dump_to_file(stream: Generator[str, None, None], out: TextIO):
out.writelines(stream)
def _write_atoms(self, file_out: TextIO) -> None:
atom_header = get_resource("cif_templates/atom_header.txt").read_text()
file_out.write(atom_header)
file_out.writelines(self.atoms)
def _writelines_to(f: TextIO, data: Sequence[str]):
f.writelines(data)
def write(self, source: StringSourceContents, output: TextIO) -> None:
with source.as_lines as lines:
output.writelines(self._transformer_function(lines))
def write_to(self, output: TextIO):
with self.as_lines as lines:
output.writelines(lines)
def write_hash_file(fp: TextIO, records: Iterable[HashFileRecord]) -> None:
fp.writelines(f"{record.digest} {record.path}\n" for record in records)
