code
string | signature
string | docstring
string | loss_without_docstring
float64 | loss_with_docstring
float64 | factor
float64 |
|---|---|---|---|---|---|
m = (
"\n"
"######################################################################################\n" # noqa
"# #\n" # noqa
"# Your version of Python appears to be out of date and lack important security #\n" # noqa
"# features. Please update to Python >= 2.7.9 or `pip install requests[security]`. #\n" # noqa
"# #\n" # noqa
"# InsecurePlatformWarning: A true SSLContext object is not available. This #\n" # noqa
"# prevents urllib3 from configuring SSL appropriately and may cause certain #\n" # noqa
"# SSL connections to fail. For more information, see #\n" # noqa
"# https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning. #\n" # noqa
"# #\n" # noqa
"######################################################################################\n"
) # noqa
if is_insecure_platform():
click.echo(m, err=True)
return True
else:
cli_log.debug("Python SSLContext passed")
return False
|
def warn_if_insecure_platform()
|
Produces a nice message if SSLContext object is not available.
Also returns True -> platform is insecure
False -> platform is secure
| 3.468157
| 3.261243
| 1.063446
|
r = requests.get(url, stream=True)
if r.status_code != 200:
cli_log.error("Failed to download file: %s" % r.json()["message"])
local_full_path = get_download_dest(input_path, r.url)
original_filename = os.path.split(local_full_path)[-1]
with open(local_full_path, "wb") as f:
click.echo("Downloading {}".format(original_filename), err=True)
for chunk in r.iter_content(chunk_size=1024):
if chunk: # filter out keep-alive new chunks
f.write(chunk)
f.flush()
pprint("Successfully downloaded %s to %s" % (original_filename, local_full_path), True)
|
def download_file_helper(url, input_path)
|
Manages the chunked downloading of a file given an url
| 2.392796
| 2.393686
| 0.999628
|
for ext in SUPPORTED_EXTENSIONS:
if f.endswith(ext):
return True
log.error("Failed upload: Not an allowed file extension: %s", f)
raise SystemExit
|
def check_for_allowed_file(f)
|
Checks a file extension against a list of seq file exts
| 5.155034
| 5.281613
| 0.976034
|
home_dir = os.path.expanduser("~")
abs_path = os.path.abspath(fp)
return abs_path.replace(home_dir, "~")
|
def collapse_user(fp)
|
Converts a path back to ~/ from expanduser()
| 2.887978
| 2.4721
| 1.168229
|
@wraps(fn)
def telemetry_wrapper(*args, **kwargs):
# By default, do not instantiate a client,
# and inherit the telemetry settings passed
client = None
if len(args) > 0 and isinstance(args[0], click.Context):
ctx = args[0]
# First try to get off API obj
if ctx.obj and ctx.obj.get("API") is not None:
client = ctx.obj["API"]._raven_client
# Else try to see if telemetry param is set
elif ctx.params.get("telemetry", False):
client = get_raven_client()
# Finally check for the ctx.obj['TELEMETRY'] bool
elif ctx.obj and ctx.obj.get("TELEMETRY", False):
client = get_raven_client()
try:
return fn(*args, **kwargs)
except Exception as e:
if client:
client.captureException()
client.context.clear()
sys.stdout = StringIO()
raise e
return telemetry_wrapper
|
def telemetry(fn)
|
Decorator for CLI and other functions that need special Sentry client handling.
This function is only required for functions that may exit *before* we set up
the ._raven_client object on the Api instance *or* that specifically catch and re-raise
exceptions or call sys.exit directly.
Note that this also overwrites verbose Raven logs on exit ("Sentry is waiting to send..."),
see https://github.com/getsentry/raven-python/issues/904 for more details.
| 3.892829
| 3.581196
| 1.087019
|
@wraps(fn)
def pretty_errors_wrapper(*args, **kwargs):
try:
fn(*args, **kwargs)
except (OneCodexException, UploadException) as e:
sys.stderr.write("\nERROR: {}".format(e))
sys.stderr.write("\nPlease feel free to contact us for help at help@onecodex.com\n\n")
sys.exit(1)
return pretty_errors_wrapper
|
def pretty_errors(fn)
|
Decorator for the CLI for catching errors and then calling sys.exit(1).
For now, this is intended for use with the CLI and scripts where we only use
OneCodexExceptions (incl. ValidationError) and UploadException.
| 3.341371
| 2.489307
| 1.34229
|
try:
atexit.unregister(func, *args, **kwargs)
except AttributeError:
# This code runs in Python 2.7 *only*
# Only replace with a noop, don't delete during iteration
for i in range(len(atexit._exithandlers)):
if atexit._exithandlers[i] == (func, args, kwargs):
atexit._exithandlers[i] = (lambda: None, [], {})
break
|
def atexit_unregister(func, *args, **kwargs)
|
Python 2/3 compatible method for unregistering exit function.
Python2 has no atexit.unregister function :/
| 3.387188
| 3.376664
| 1.003117
|
from skbio.tree import TreeNode
# build all the nodes
nodes = {}
for tax_id in self.taxonomy.index:
node = TreeNode(name=tax_id, length=1)
node.tax_name = self.taxonomy["name"][tax_id]
node.rank = self.taxonomy["rank"][tax_id]
node.parent_tax_id = self.taxonomy["parent_tax_id"][tax_id]
nodes[tax_id] = node
# generate all the links
for tax_id in self.taxonomy.index:
try:
parent = nodes[nodes[tax_id].parent_tax_id]
except KeyError:
if tax_id != "1":
warnings.warn(
"tax_id={} has parent_tax_id={} which is not in tree"
"".format(tax_id, nodes[tax_id].parent_tax_id)
)
continue
parent.append(nodes[tax_id])
return nodes["1"]
|
def tree_build(self)
|
Build a tree from the taxonomy data present in this `ClassificationsDataFrame` or
`SampleCollection`.
Returns
-------
`skbio.tree.TreeNode`, the root node of a tree that contains all the taxa in the current
analysis and their parents leading back to the root node.
| 2.532822
| 2.492864
| 1.016029
|
tax_ids_to_keep = []
for tax_id in tax_ids:
tax_ids_to_keep.append(tax_id)
tax_ids_to_keep.extend([x.name for x in tree.find(tax_id).ancestors()])
tree = tree.copy()
tree.remove_deleted(lambda n: n.name not in tax_ids_to_keep)
return tree
|
def tree_prune_tax_ids(self, tree, tax_ids)
|
Prunes a tree back to contain only the tax_ids in the list and their parents.
Parameters
----------
tree : `skbio.tree.TreeNode`
The root node of the tree to perform this operation on.
tax_ids : `list`
A `list` of taxonomic IDs to keep in the tree.
Returns
-------
`skbio.tree.TreeNode`, the root of a tree containing the given taxonomic IDs and their
parents, leading back to the root node.
| 2.862686
| 3.265022
| 0.876774
|
if rank is None:
return tree.copy()
tree = tree.copy()
for node in tree.postorder():
if node.rank == rank:
node._above_rank = True
elif any([getattr(n, "_above_rank", False) for n in node.children]):
node._above_rank = True
else:
node._above_rank = False
tree.remove_deleted(lambda n: not getattr(n, "_above_rank", False))
return tree
|
def tree_prune_rank(self, tree, rank="species")
|
Takes a TreeNode tree and prunes off any tips not at the specified rank and backwards up
until all of the tips are at the specified rank.
Parameters
----------
tree : `skbio.tree.TreeNode`
The root node of the tree to perform this operation on.
rank : {kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'}, optional
Analysis will be restricted to abundances of taxa at the specified level.
Returns
-------
`skbio.tree.TreeNode`, the root of the tree where all tips are at the given rank, and all
tips have a path back to the root node.
Examples
--------
tree_prune_rank(tree, 'species') will remove all subspecies/strain nodes and return a tree
containing all genus-level nodes and higher.
| 3.28399
| 3.866724
| 0.849295
|
f = open_strings_file(file_path, "w")
for element in file_elements:
f.write(unicode(element))
f.write(u"\n")
f.close()
|
def write_file_elements_to_strings_file(file_path, file_elements)
|
Write elements to the string file
Args:
file_path (str): The path to the strings file
file_elements (list) : List of elements to write to the file.
| 2.877485
| 3.221453
| 0.893226
|
logging_level = logging.WARNING
if args is not None and args.verbose:
logging_level = logging.INFO
config = {"level": logging_level, "format": "jtlocalize:%(message)s"}
if args is not None and args.log_path != "":
config["filename"] = args.log_path
logging.basicConfig(**config)
|
def setup_logging(args=None)
|
Setup logging module.
Args:
args (optional): The arguments returned by the argparse module.
| 3.63731
| 4.457083
| 0.816074
|
localization_dictionary = {}
f = open_strings_file(file_path, "r+")
header_comment_key_value_tuples = extract_header_comment_key_value_tuples_from_file(f)
if len(header_comment_key_value_tuples) == 0:
logging.warning("Couldn't find any strings in file '%s'. Check encoding and format." % file_path)
for header_comment, comments, key, value in header_comment_key_value_tuples:
localization_entry = LocalizationEntry(comments, key, value)
localization_dictionary[
localization_entry.__getattribute__(localization_entry_attribute_name_for_key)] = localization_entry
f.close()
return localization_dictionary
|
def __generate_localization_dictionary_from_file(file_path, localization_entry_attribute_name_for_key)
|
Generates a dictionary mapping between keys (defined by the given attribute name) and localization entries.
Args:
file_path (str): The strings file path.
localization_entry_attribute_name_for_key: The name of the attribute of LocalizationEntry to use as key.
Returns:
dict: A dictionary mapping between keys (defined by the given attribute name) and localization entries.
| 2.978773
| 3.031299
| 0.982672
|
file_data = file_descriptor.read()
findall_result = re.findall(HEADER_COMMENT_KEY_VALUE_TUPLES_REGEX, file_data, re.MULTILINE | re.DOTALL)
returned_list = []
for header_comment, _ignored, raw_comments, key, value in findall_result:
comments = re.findall("/\* (.*?) \*/", raw_comments)
if len(comments) == 0:
comments = [u""]
returned_list.append((header_comment, comments, key, value))
return returned_list
|
def extract_header_comment_key_value_tuples_from_file(file_descriptor)
|
Extracts tuples representing comments and localization entries from strings file.
Args:
file_descriptor (file): The file to read the tuples from
Returns:
list : List of tuples representing the headers and localization entries.
| 3.320256
| 3.604576
| 0.921123
|
result_pairs = re.findall(JTL_REGEX, open(file_path).read())
for result_key, result_comment in result_pairs:
results_dict[result_key] = result_comment
return results_dict
|
def extract_jtl_string_pairs_from_text_file(results_dict, file_path)
|
Extracts all string pairs matching the JTL pattern from given text file.
This can be used as an "extract_func" argument in the extract_string_pairs_in_directory method.
Args:
results_dict (dict): The dict to add the the string pairs to.
file_path (str): The path of the file from which to extract the string pairs.
| 3.201223
| 3.614239
| 0.885725
|
result = {}
for root, dirnames, filenames in os.walk(directory_path):
for file_name in filenames:
if filter_func(file_name):
file_path = os.path.join(root, file_name)
try:
extract_func(result, file_path)
except Exception as e:
print "Error in file " + file_name
print e
return result
|
def extract_string_pairs_in_directory(directory_path, extract_func, filter_func)
|
Retrieves all string pairs in the directory
Args:
directory_path (str): The path of the directory containing the file to extract string pairs from.
extract_func (function): Function for extracting the localization keys and comments from the files.
The extract function receives 2 parameters:
- dict that the keys (a key in the dict) and comments (a value in the dict) are added to.
- str representing file path
filter_func (function): Function for filtering files in the directory.
The filter function receives the file name and returns a bool representing the filter result.
True if the file name passed the filter, False otherwise.
Returns:
dict: A mapping between string pairs first value (probably the key), and the second value (probably the comment).
| 2.004736
| 2.035091
| 0.985084
|
escaped_key = re.sub(r'([^\\])"', '\\1\\"', entry_key)
file_descriptor.write(u'/* %s */\n' % entry_comment)
file_descriptor.write(u'"%s" = "%s";\n' % (escaped_key, escaped_key))
|
def write_entry_to_file(file_descriptor, entry_comment, entry_key)
|
Writes a localization entry to the file
Args:
file_descriptor (file, instance): The file to write the entry to.
entry_comment (str): The entry's comment.
entry_key (str): The entry's key.
| 2.772626
| 2.890321
| 0.95928
|
output_file = open_strings_file(file_path, "a")
write_section_header_to_file(output_file, section_name)
for entry_key, entry_comment in sorted(localization_key_to_comment.iteritems(), key=operator.itemgetter(1)):
output_file.write(u'\n')
write_entry_to_file(output_file, entry_comment, entry_key)
output_file.close()
|
def append_dictionary_to_file(localization_key_to_comment, file_path, section_name)
|
Appends dictionary of localization keys and comments to a file
Args:
localization_key_to_comment (dict): A mapping between localization keys and comments.
file_path (str): The path of the file to append to.
section_name (str): The name of the section.
| 2.482225
| 2.768138
| 0.896713
|
output_file_descriptor = open_strings_file(file_name, "w")
for entry_key, entry_comment in sorted(localization_key_to_comment.iteritems(), key=operator.itemgetter(1)):
write_entry_to_file(output_file_descriptor, entry_comment, entry_key)
output_file_descriptor.write(u'\n')
output_file_descriptor.close()
|
def write_dict_to_new_file(file_name, localization_key_to_comment)
|
Writes dictionary of localization keys and comments to a file.
Args:
localization_key_to_comment (dict): A mapping between localization keys and comments.
file_name (str): The path of the file to append to.
| 2.74567
| 2.959373
| 0.927788
|
result = []
for root, dir_names, file_names in os.walk(base_dir):
for filename in file_names:
candidate = os.path.join(root, filename)
if should_include_file_in_search(candidate, extensions, exclude_dirs):
result.append(candidate)
return result
|
def find_files(base_dir, extensions, exclude_dirs=list())
|
Find all files matching the given extensions.
Args:
base_dir (str): Path of base directory to search in.
extensions (list): A list of file extensions to search for.
exclude_dirs (list): A list of directories to exclude from search.
Returns:
list of paths that match the search
| 2.251952
| 2.608161
| 0.863425
|
return (exclude_dirs is None or not any(file_name.startswith(d) for d in exclude_dirs)) and \
any(file_name.endswith(e) for e in extensions)
|
def should_include_file_in_search(file_name, extensions, exclude_dirs)
|
Whether or not a filename matches a search criteria according to arguments.
Args:
file_name (str): A file path to check.
extensions (list): A list of file extensions file should match.
exclude_dirs (list): A list of directories to exclude from search.
Returns:
A boolean of whether or not file matches search criteria.
| 2.315329
| 3.375475
| 0.685927
|
if rank == "auto":
# if we're an accessor for a ClassificationsDataFrame, use its _rank property
if self.__class__.__name__ == "OneCodexAccessor":
return self._rank
if self._field == "abundance":
return "species"
else:
return "genus"
else:
return rank
|
def _get_auto_rank(self, rank)
|
Tries to figure out what rank we should use for analyses
| 10.174273
| 9.023121
| 1.127578
|
return (
getattr(self, "_normalized", False)
or getattr(self, "_field", None) == "abundance"
or bool((self._results.sum(axis=1).round(4) == 1.0).all())
)
|
def _guess_normalized(self)
|
Returns true if the collated counts in `self._results` appear to be normalized.
Notes
-----
It's possible that the _results df has already been normalized, which can cause some
methods to fail. This method lets us guess whether that's true and act accordingly.
| 6.573182
| 4.820864
| 1.363486
|
from onecodex.dataframes import ClassificationsDataFrame
rank = self._get_auto_rank(rank)
df = self._results.copy()
# subset by taxa
if rank:
if rank == "kingdom":
warnings.warn(
"Did you mean to specify rank=kingdom? Use rank=superkingdom to see Bacteria, "
"Archaea and Eukaryota."
)
tax_ids_to_keep = []
for tax_id in df.keys():
if self.taxonomy["rank"][tax_id] == rank:
tax_ids_to_keep.append(tax_id)
if len(tax_ids_to_keep) == 0:
raise OneCodexException("No taxa kept--is rank ({}) correct?".format(rank))
df = df.loc[:, tax_ids_to_keep]
# normalize
if normalize is False and self._guess_normalized():
raise OneCodexException("Data has already been normalized and this can not be undone.")
if normalize is True or (
normalize == "auto" and rank is not None and self._field != "abundance"
):
df = df.div(df.sum(axis=1), axis=0)
# remove columns (tax_ids) with no values that are > 0
if remove_zeros:
df = df.loc[:, (df != 0).any(axis=0)]
# restrict to taxa appearing in one or more samples at the given threshold
if threshold:
df = df.loc[:, df.max() >= threshold]
# restrict to N most abundant taxa
if top_n:
idx = df.sum(axis=0).sort_values(ascending=False).head(top_n).index
df = df.loc[:, idx]
# additional data to copy into the ClassificationsDataFrame
ocx_data = {
"ocx_metadata": self.metadata.copy(),
"ocx_rank": rank,
"ocx_field": self._field,
"ocx_taxonomy": self.taxonomy.copy(),
"ocx_normalized": normalize,
}
# generate long-format table
if table_format == "long":
long_df = {"classification_id": [], "tax_id": [], self._field: []}
for t_id in df:
for c_id, count in df[t_id].iteritems():
long_df["classification_id"].append(c_id)
long_df["tax_id"].append(t_id)
long_df[self._field].append(count)
results_df = ClassificationsDataFrame(long_df, **ocx_data)
elif table_format == "wide":
results_df = ClassificationsDataFrame(df, **ocx_data)
else:
raise OneCodexException("table_format must be one of: long, wide")
return results_df
|
def to_df(
self,
rank="auto",
top_n=None,
threshold=None,
remove_zeros=True,
normalize="auto",
table_format="wide",
)
|
Takes the ClassificationsDataFrame associated with these samples, or SampleCollection,
does some filtering, and returns a ClassificationsDataFrame copy.
Parameters
----------
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'}, optional
Analysis will be restricted to abundances of taxa at the specified level.
top_n : `integer`, optional
Return only the top N most abundant taxa.
threshold : `float`, optional
Return only taxa more abundant than this threshold in one or more samples.
remove_zeros : `bool`, optional
Do not return taxa that have zero abundance in every sample.
normalize : {'auto', True, False}
Convert read counts to relative abundances (each sample sums to 1.0).
table_format : {'long', 'wide'}
If wide, rows are classifications, cols are taxa, elements are counts. If long, rows are
observations with three cols each: classification_id, tax_id, and count.
Returns
-------
`ClassificationsDataFrame`
| 3.000726
| 2.948483
| 1.017719
|
from weasyprint import HTML, CSS
nb = copy.deepcopy(nb)
output, resources = super(OneCodexPDFExporter, self).from_notebook_node(
nb, resources=resources, **kw
)
buf = BytesIO()
HTML(string=output).write_pdf(
buf, stylesheets=[CSS(os.path.join(ASSETS_PATH, CSS_TEMPLATE_FILE))]
)
buf.seek(0)
return buf.read(), resources
|
def from_notebook_node(self, nb, resources=None, **kw)
|
Takes output of OneCodexHTMLExporter and runs Weasyprint to get a PDF.
| 3.583723
| 2.6554
| 1.349598
|
output, resources = super(OneCodexDocumentExporter, self).from_notebook_node(
nb, resources=resources, **kw
)
from onecodex import Api
from onecodex.lib.upload import upload_document_fileobj
ocx = Api()
default_filename = "Analysis Report - {dt:%B} {dt.day}, {dt:%Y}".format(
dt=datetime.datetime.now()
)
file_name = resources["metadata"].get("one_codex_doc_portal_filename", default_filename)
try:
document_id = upload_document_fileobj(
BytesIO(output), file_name, ocx._client.session, ocx.Documents._resource
)
except UploadException as exc:
resp = json.dumps({"status": 500, "message": str(exc)})
return resp, resources
except Exception:
resp = json.dumps(
{
"status": 500,
"message": "Upload failed. Please contact help@onecodex.com for assistance.",
}
)
return resp, resources
resp = json.dumps({"status": 200, "document_id": document_id})
return resp, resources
|
def from_notebook_node(self, nb, resources=None, **kw)
|
Takes PDF output from PDFExporter and uploads to One Codex Documents portal.
| 3.554503
| 3.163188
| 1.123709
|
localization_directory = os.path.join(localization_bundle_path, DEFAULT_LANGUAGE_DIRECTORY_NAME)
if not os.path.exists(localization_directory):
os.makedirs(localization_directory)
localization_file = os.path.join(localization_directory, LOCALIZATION_FILENAME)
# Creating the same directory tree structure in the tmp directory
tmp_localization_directory = os.path.join(tmp_directory, DEFAULT_LANGUAGE_DIRECTORY_NAME)
tmp_localization_file = os.path.join(tmp_localization_directory, LOCALIZATION_FILENAME)
if os.path.isdir(tmp_localization_directory):
shutil.rmtree(tmp_localization_directory)
os.mkdir(tmp_localization_directory)
logging.info("Running genstrings")
source_files = extract_source_files(project_base_dir, exclude_dirs)
genstrings_cmd = 'genstrings -s JTLocalizedString -o %s %s' % (tmp_localization_directory, " ".join(
['"%s"' % (source_file,) for source_file in source_files]))
genstrings_process = subprocess.Popen(genstrings_cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE,
stdin=subprocess.PIPE, shell=True)
genstrings_out, genstrings_err = genstrings_process.communicate()
remove_empty_comments_from_file(tmp_localization_file)
add_genstrings_comments_to_file(tmp_localization_file, genstrings_err)
genstrings_rc = genstrings_process.returncode
if genstrings_rc != 0:
logging.fatal("genstrings returned %d, aborting run!", genstrings_rc)
sys.exit(genstrings_rc)
create_localized_strings_from_ib_files(project_base_dir, exclude_dirs, tmp_localization_file,
special_ui_components_prefix)
if include_strings_file:
target = open_strings_file(tmp_localization_file, "a")
source = open_strings_file(include_strings_file, "r")
target.write(source.read())
source.close()
target.close()
handle_duplications(tmp_localization_file)
if os.path.isfile(localization_file):
logging.info("Merging old localizable with new one...")
merge_strings_files(localization_file, tmp_localization_file)
else:
logging.info("No Localizable yet, moving the created file...")
shutil.move(tmp_localization_file, localization_file)
|
def generate_strings(project_base_dir, localization_bundle_path, tmp_directory, exclude_dirs, include_strings_file,
special_ui_components_prefix)
|
Calls the builtin 'genstrings' command with JTLocalizedString as the string to search for,
and adds strings extracted from UI elements internationalized with 'JTL' + removes duplications.
| 2.456392
| 2.411512
| 1.018611
|
if callable(filter_func):
return self.__class__([obj for obj in self if filter_func(obj) is True], **self._kwargs)
else:
raise OneCodexException(
"Expected callable for filter, got: {}".format(type(filter_func).__name__)
)
|
def filter(self, filter_func)
|
Return a new SampleCollection containing only samples meeting the filter criteria.
Will pass any kwargs (e.g., field or skip_missing) used when instantiating the current class
on to the new SampleCollection that is returned.
Parameters
----------
filter_func : `callable`
A function that will be evaluated on every object in the collection. The function must
return a `bool`. If True, the object will be kept. If False, it will be removed from the
SampleCollection that is returned.
Returns
-------
`onecodex.models.SampleCollection` containing only objects `filter_func` returned True on.
Examples
--------
Generate a new collection of Samples that have a specific filename extension:
new_collection = samples.filter(lambda s: s.filename.endswith('.fastq.gz'))
| 3.913597
| 5.080237
| 0.770357
|
skip_missing = skip_missing if skip_missing else self._kwargs["skip_missing"]
new_classifications = []
for a in self._res_list:
if a.__class__.__name__ == "Samples":
c = a.primary_classification
elif a.__class__.__name__ == "Classifications":
c = a
else:
raise OneCodexException(
"Objects in SampleCollection must be one of: Classifications, Samples"
)
if skip_missing and not c.success:
warnings.warn("Classification {} not successful. Skipping.".format(c.id))
continue
new_classifications.append(c)
self._cached["classifications"] = new_classifications
|
def _classification_fetch(self, skip_missing=None)
|
Turns a list of objects associated with a classification result into a list of
Classifications objects.
Parameters
----------
skip_missing : `bool`
If an analysis was not successful, exclude it, warn, and keep going
Returns
-------
None, but stores a result in self._cached.
| 3.925309
| 3.78436
| 1.037245
|
import pandas as pd
DEFAULT_FIELDS = None
metadata = []
for c in self._classifications:
m = c.sample.metadata
if DEFAULT_FIELDS is None:
DEFAULT_FIELDS = list(m._resource._schema["properties"].keys())
DEFAULT_FIELDS.remove("$uri")
DEFAULT_FIELDS.remove("sample")
metadatum = {f: getattr(m, f) for f in DEFAULT_FIELDS}
metadatum["classification_id"] = c.id
metadatum["sample_id"] = m.sample.id
metadatum["metadata_id"] = m.id
metadatum["created_at"] = m.sample.created_at
metadatum["filename"] = c.sample.filename
metadatum.update(m.custom)
metadata.append(metadatum)
if metadata:
metadata = pd.DataFrame(metadata).set_index("classification_id")
else:
metadata = pd.DataFrame(
columns=["classification_id", "sample_id", "metadata_id", "created_at"]
)
self._cached["metadata"] = metadata
|
def _collate_metadata(self)
|
Turns a list of objects associated with a classification result into a DataFrame of
metadata.
Returns
-------
None, but stores a result in self._cached.
| 2.943778
| 2.792351
| 1.054229
|
import pandas as pd
field = field if field else self._kwargs["field"]
if field not in ("auto", "abundance", "readcount", "readcount_w_children"):
raise OneCodexException("Specified field ({}) not valid.".format(field))
# we'll fill these dicts that eventually turn into DataFrames
df = {"classification_id": [c.id for c in self._classifications]}
tax_info = {"tax_id": [], "name": [], "rank": [], "parent_tax_id": []}
if field == "auto":
field = "readcount_w_children"
self._cached["field"] = field
for c_idx, c in enumerate(self._classifications):
# pulling results from mainline is the slowest part of the function
result = c.results()["table"]
# d contains info about a taxon in result, including name, id, counts, rank, etc.
for d in result:
d_tax_id = d["tax_id"]
if d_tax_id not in tax_info["tax_id"]:
for k in ("tax_id", "name", "rank", "parent_tax_id"):
tax_info[k].append(d[k])
# first time we've seen this taxon, so make a vector for it
df[d_tax_id] = [0] * len(self._classifications)
df[d_tax_id][c_idx] = d[field]
# format as a Pandas DataFrame
df = pd.DataFrame(df).set_index("classification_id").fillna(0)
df.columns.name = "tax_id"
tax_info = pd.DataFrame(tax_info).set_index("tax_id")
self._cached["results"] = df
self._cached["taxonomy"] = tax_info
|
def _collate_results(self, field=None)
|
For a list of objects associated with a classification result, return the results as a
DataFrame and dict of taxa info.
Parameters
----------
field : {'readcount_w_children', 'readcount', 'abundance'}
Which field to use for the abundance/count of a particular taxon in a sample.
- 'readcount_w_children': total reads of this taxon and all its descendants
- 'readcount': total reads of this taxon
- 'abundance': genome size-normalized relative abundances, from shotgun sequencing
Returns
-------
None, but stores a result in self._cached.
| 3.984714
| 3.493109
| 1.140736
|
otu_format = "Biological Observation Matrix 1.0.0"
# Note: This is exact format URL is required by https://github.com/biocore/biom-format
otu_url = "http://biom-format.org"
otu = OrderedDict(
{
"id": biom_id,
"format": otu_format,
"format_url": otu_url,
"type": "OTU table",
"generated_by": "One Codex API V1",
"date": datetime.now().isoformat(),
"rows": [],
"columns": [],
"matrix_type": "sparse",
"matrix_element_type": "int",
}
)
rows = defaultdict(dict)
tax_ids_to_names = {}
for classification in self._classifications:
col_id = len(otu["columns"]) # 0 index
# Re-encoding the JSON is a bit of a hack, but
# we need a ._to_dict() method that properly
# resolves references and don't have one at the moment
columns_entry = {
"id": str(classification.id),
"sample_id": str(classification.sample.id),
"sample_filename": classification.sample.filename,
"metadata": json.loads(
classification.sample.metadata._to_json(include_references=False)
),
}
otu["columns"].append(columns_entry)
sample_df = classification.table()
for row in sample_df.iterrows():
tax_id = row[1]["tax_id"]
tax_ids_to_names[tax_id] = row[1]["name"]
rows[tax_id][col_id] = int(row[1]["readcount"])
num_rows = len(rows)
num_cols = len(otu["columns"])
otu["shape"] = [num_rows, num_cols]
otu["data"] = []
for present_taxa in sorted(rows):
# add the row entry
row_id = len(otu["rows"])
otu["rows"].append(
{"id": present_taxa, "metadata": {"taxonomy": tax_ids_to_names[present_taxa]}}
)
for sample_with_hit in rows[present_taxa]:
counts = rows[present_taxa][sample_with_hit]
otu["data"].append([row_id, sample_with_hit, counts])
return otu
|
def to_otu(self, biom_id=None)
|
Converts a list of objects associated with a classification result into a `dict` resembling
an OTU table.
Parameters
----------
biom_id : `string`, optional
Optionally specify an `id` field for the generated v1 BIOM file.
Returns
-------
otu_table : `OrderedDict`
A BIOM OTU table, returned as a Python OrderedDict (can be dumped to JSON)
| 3.210745
| 3.149074
| 1.019584
|
output_file_elements = []
old_translated_file_dict = generate_localization_key_to_entry_dictionary_from_file(old_translated_file)
new_translated_file_dict = generate_localization_key_to_entry_dictionary_from_file(new_translated_file)
f = open_strings_file(updated_localizable_file, "r")
for header_comment, comments, key, value in extract_header_comment_key_value_tuples_from_file(f):
translation_value = None
if len(header_comment) > 0:
output_file_elements.append(Comment(header_comment))
if value in new_translated_file_dict:
translation_value = new_translated_file_dict[value].value
elif key in old_translated_file_dict:
translation_value = old_translated_file_dict[key].value
elif key in new_translated_file_dict:
translation_value = new_translated_file_dict[key].value
if translation_value is not None:
output_file_elements.append(LocalizationEntry(comments, key, translation_value))
f.close()
write_file_elements_to_strings_file(merged_translated_file, output_file_elements)
|
def localization_merge_back(updated_localizable_file, old_translated_file, new_translated_file, merged_translated_file)
|
Generates a file merging the old translations and the new ones.
Args:
updated_localizable_file (str): The path to the updated localization strings file, meaning the strings that
require translation.
old_translated_file (str): The path to the strings file containing the previously translated strings.
new_translated_file (str): The path to the strings file containing the newly translated strings.
merged_translated_file (str): The path to the output file with the merged translations.
| 2.22937
| 2.283986
| 0.976087
|
# must be one of Nominal, Ordinal, Time per altair
if category_type not in ("N", "O", "T"):
raise OneCodexException("If specifying category_type, must be N, O, or T")
# adapted from https://altair-viz.github.io/gallery/boxplot_max_min.html
lower_box = "q1({}):Q".format(quantity)
lower_whisker = "min({}):Q".format(quantity)
upper_box = "q3({}):Q".format(quantity)
upper_whisker = "max({}):Q".format(quantity)
if category_type == "T":
x_format = "hoursminutes({}):{}".format(category, category_type)
else:
x_format = "{}:{}".format(category, category_type)
lower_plot = (
alt.Chart(df)
.mark_rule()
.encode(y=alt.Y(lower_whisker, axis=alt.Axis(title=ylabel)), y2=lower_box, x=x_format)
)
middle_plot = alt.Chart(df).mark_bar(size=35).encode(y=lower_box, y2=upper_box, x=x_format)
upper_plot = alt.Chart(df).mark_rule().encode(y=upper_whisker, y2=upper_box, x=x_format)
middle_tick = (
alt.Chart(df)
.mark_tick(color="black", size=35)
.encode(
y="median({}):Q".format(quantity),
x=alt.X(x_format, axis=alt.Axis(title=xlabel), scale=alt.Scale(rangeStep=45)),
tooltip="median({}):Q".format(quantity),
)
)
chart = lower_plot + middle_plot + upper_plot + middle_tick
if title:
chart = chart.properties(title=title)
return chart
|
def boxplot(df, category, quantity, category_type="N", title=None, xlabel=None, ylabel=None)
|
Plot a simple boxplot using Altair.
Parameters
----------
df : `pandas.DataFrame`
Contains columns matching 'category' and 'quantity' labels, at a minimum.
category : `string`
The name of the column in df used to group values on the horizontal axis.
quantity : `string`
The name of the columm in df of values to plot on the vertical axis. Must be numerical.
category_type : {'N', 'O', 'T'}, optional
Nominal, ordinal, or time values can be used as categories. Quantitative (Q) values look weird.
title : `string`, optional
Text label at the top of the plot.
xlabel : `string`, optional
Text label along the horizontal axis.
ylabel : `string`, optional
Text label along the vertical axis.
Returns
-------
`altair.Chart`
| 2.573413
| 2.575373
| 0.999239
|
plot_data = {
"x": [],
"y": [],
"o": [], # order these points should be connected in
"b": [], # one number per branch
}
for idx, (i, d) in enumerate(zip(tree["icoord"], tree["dcoord"])):
plot_data["x"].extend(map(lambda x: -x, d))
plot_data["y"].extend(map(lambda x: -x, i))
plot_data["o"].extend([0, 1, 2, 3])
plot_data["b"].extend([idx] * 4)
plot_data = pd.DataFrame(plot_data)
chart = (
alt.Chart(plot_data, width=100, height=15 * len(tree["leaves"]) - 7.5)
.mark_line(point=False, opacity=0.5)
.encode(
x=alt.X("x", axis=None),
y=alt.Y("y", axis=None, scale=alt.Scale(zero=True, nice=False)),
order="o",
color=alt.Color(
"b:N",
scale=alt.Scale(domain=list(range(idx + 1)), range=["black"] * (idx + 1)),
legend=None,
),
)
)
return chart
|
def dendrogram(tree)
|
Plot a simple square dendrogram using Altair.
Parameters
----------
tree : `dict` returned by `scipy.cluster.hierarchy.dendrogram`
Contains, at a minimum, 'icoord', 'dcoord', and 'leaves' keys. Scipy does all the work of
determining where the lines in the tree should go. All we have to do is draw them.
Returns
-------
`altair.Chart`
| 2.632316
| 2.478007
| 1.062271
|
errors_to_log = [line for line in genstrings_err.splitlines() if "used with multiple comments" not in line]
if len(errors_to_log) > 0:
logging.warning("genstrings warnings:\n%s", "\n".join(errors_to_log))
loc_file = open_strings_file(localization_file, "a")
regex_matches = re.findall(r'Warning: Key "(.*?)" used with multiple comments ("[^"]*" (& "[^"]*")+)',
genstrings_err)
logging.info("Adding multiple comments from genstrings output")
for regex_match in regex_matches:
if len(regex_match) == 3:
key = regex_match[0]
comments = [comment.strip()[1:-1] for comment in regex_match[1].split("&")]
logging.info("Found key with %d comments: %s", len(comments), key)
loc_key = LocalizationEntry(comments, key, key)
loc_file.write(unicode(loc_key))
loc_file.write(u"\n")
loc_file.close()
|
def add_genstrings_comments_to_file(localization_file, genstrings_err)
|
Adds the comments produced by the genstrings script for duplicate keys.
Args:
localization_file (str): The path to the strings file.
| 3.479562
| 3.48398
| 0.998732
|
if path and file_obj:
raise OneCodexException("Please specify only one of: path, file_obj")
if path is None and file_obj is None:
path = os.path.join(os.getcwd(), self.filename)
if path and os.path.exists(path):
raise OneCodexException("{} already exists! Will not overwrite.".format(path))
try:
url_data = self._resource.download_uri()
resp = requests.get(url_data["download_uri"], stream=True)
with (open(path, "wb") if path else file_obj) as f_out:
if progressbar:
with click.progressbar(length=self.size, label=self.filename) as bar:
for data in resp.iter_content(chunk_size=1024):
bar.update(len(data))
f_out.write(data)
else:
for data in resp.iter_content(chunk_size=1024):
f_out.write(data)
except KeyboardInterrupt:
if path:
os.remove(path)
raise
except requests.exceptions.HTTPError as exc:
if exc.response.status_code == 401:
raise OneCodexException("You must be logged in to download files.")
elif exc.response.status_code == 402:
raise OneCodexException(
"You must either have a premium platform account or be in "
"a notebook environment to download files."
)
elif exc.response.status_code == 403:
raise OneCodexException("You are not authorized to download this file.")
else:
raise OneCodexException(
"Download failed with an HTTP status code {}.".format(exc.response.status_code)
)
return path
|
def download(self, path=None, file_obj=None, progressbar=False)
|
Downloads files from One Codex.
Parameters
----------
path : `string`, optional
Full path to save the file to. If omitted, defaults to the original filename
in the current working directory.
file_obj : file-like object, optional
Rather than save the file to a path, write it to this file-like object.
progressbar : `bool`
Display a progress bar using Click for the download?
Returns
-------
`string`
The path the file was downloaded to, if applicable. Otherwise, None.
Notes
-----
If no arguments specified, defaults to download the file as the original filename
in the current working directory. If `file_obj` given, will write data into the
passed file-like object. If `path` given, will download the file to the path provided,
but will not overwrite any existing files.
| 2.225535
| 2.198076
| 1.012493
|
res = cls._resource
doc_id = upload_document(file_path, res._client.session, res, progressbar=progressbar)
return cls.get(doc_id)
|
def upload(cls, file_path, progressbar=None)
|
Uploads a series of files to the One Codex server.
Parameters
----------
file_path : `string`
A path to a file on the system.
progressbar : `click.progressbar`, optional
If passed, display a progress bar using Click.
Returns
-------
A `Samples` object upon successful upload. None if the upload failed.
| 6.947553
| 11.498992
| 0.604188
|
logging.info("Preparing for translation..")
for strings_file in os.listdir(os.path.join(localization_bundle_path, DEFAULT_LANGUAGE_DIRECTORY_NAME)):
if not strings_file.endswith(".strings"):
continue
strings_path = os.path.join(localization_bundle_path, DEFAULT_LANGUAGE_DIRECTORY_NAME, strings_file)
for lang_dir in os.listdir(localization_bundle_path):
if lang_dir == DEFAULT_LANGUAGE_DIRECTORY_NAME or lang_dir.startswith("."):
continue
dest_strings_path = os.path.join(localization_bundle_path, lang_dir, strings_file)
pending_path = dest_strings_path + ".pending"
excluded_path = dest_strings_path + ".excluded"
if not os.path.exists(dest_strings_path):
open_strings_file(dest_strings_path, "a").close()
logging.info("Preparing diff for %s in %s", lang_dir, pending_path)
localization_diff(strings_path, dest_strings_path, excluded_path, pending_path)
|
def prepare_for_translation(localization_bundle_path)
|
Prepares the localization bundle for translation.
This means, after creating the strings files using genstrings.sh, this will produce '.pending' files, that contain
the files that are yet to be translated.
Args:
localization_bundle_path (str): The path to the localization bundle.
| 2.385022
| 2.308458
| 1.033167
|
# set up the context for sub commands
click.Context.get_usage = click.Context.get_help
ctx.obj = {}
ctx.obj["API_KEY"] = api_key
ctx.obj["NOPPRINT"] = no_pprint
ctx.obj["TELEMETRY"] = telemetry
if verbose:
log.setLevel(logging.DEBUG)
# handle checking insecure platform, we let upload command do it by itself
if ctx.invoked_subcommand != "upload":
warn_if_insecure_platform()
|
def onecodex(ctx, api_key, no_pprint, verbose, telemetry)
|
One Codex v1 API command line interface
| 5.264585
| 5.3869
| 0.977294
|
if len(files) == 0:
click.echo(ctx.get_help())
return
files = list(files)
bar = click.progressbar(length=sum([_file_size(x) for x in files]), label="Uploading... ")
run_via_threadpool(
ctx.obj["API"].Documents.upload,
files,
{"progressbar": bar},
max_threads=max_threads,
graceful_exit=False,
)
|
def documents_upload(ctx, max_threads, files)
|
Upload a document file (of any type) to One Codex
| 4.239732
| 4.23181
| 1.001872
|
# basic operation -- just print
if not readlevel and not results:
cli_resource_fetcher(ctx, "classifications", classifications)
# fetch the results
elif not readlevel and results:
if len(classifications) != 1:
log.error("Can only request results data on one Classification at a time")
else:
classification = ctx.obj["API"].Classifications.get(classifications[0])
if not classification:
log.error(
"Could not find classification {} (404 status code)".format(classifications[0])
)
return
results = classification.results(json=True)
pprint(results, ctx.obj["NOPPRINT"])
# fetch the readlevel
elif readlevel is not None and not results:
if len(classifications) != 1:
log.error("Can only request read-level data on one Classification at a time")
else:
classification = ctx.obj["API"].Classifications.get(classifications[0])
if not classification:
log.error(
"Could not find classification {} (404 status code)".format(classifications[0])
)
return
tsv_url = classification._readlevel()["url"]
log.info("Downloading tsv data from: {}".format(tsv_url))
download_file_helper(tsv_url, readlevel_path)
# both given -- complain
else:
log.error("Can only request one of read-level data or results data at a time")
|
def classifications(ctx, classifications, results, readlevel, readlevel_path)
|
Retrieve performed metagenomic classifications
| 3.293757
| 3.304889
| 0.996632
|
appendables = {}
if tags:
appendables["tags"] = []
for tag in tags:
appendables["tags"].append(tag)
if metadata:
appendables["metadata"] = {}
for metadata_kv in metadata:
split_metadata = metadata_kv.split("=", 1)
if len(split_metadata) > 1:
metadata_value = split_metadata[1]
appendables["metadata"][split_metadata[0]] = metadata_value
appendables = validate_appendables(appendables, ctx.obj["API"])
if (forward or reverse) and not (forward and reverse):
click.echo("You must specify both forward and reverse files", err=True)
ctx.exit(1)
if forward and reverse:
if len(files) > 0:
click.echo(
"You may not pass a FILES argument when using the "
" --forward and --reverse options.",
err=True,
)
ctx.exit(1)
files = [(forward, reverse)]
elif len(files) == 0:
click.echo(ctx.get_help())
return
else:
files = list(files)
# "intelligently" find paired files and tuple them
paired_files = []
single_files = set(files)
for filename in files:
# convert "read 1" filenames into "read 2" and check that they exist; if they do
# upload the files as a pair, autointerleaving them
pair = re.sub("[._][Rr]1[._]", lambda x: x.group().replace("1", "2"), filename)
# we don't necessary need the R2 to have been passed in; we infer it anyways
if pair != filename and os.path.exists(pair):
if not prompt and pair not in single_files:
# if we're not prompting, don't automatically pull in files
# not in the list the user passed in
continue
paired_files.append((filename, pair))
if pair in single_files:
single_files.remove(pair)
single_files.remove(filename)
auto_pair = True
if prompt and len(paired_files) > 0:
pair_list = ""
for p in paired_files:
pair_list += "\n {} & {}".format(os.path.basename(p[0]), os.path.basename(p[1]))
answer = click.confirm(
"It appears there are paired files:{}\nInterleave them after upload?".format(
pair_list
),
default="Y",
)
if not answer:
auto_pair = False
if auto_pair:
files = paired_files + list(single_files)
total_size = sum(
[
(_file_size(x[0], uncompressed=True) + _file_size(x[1], uncompressed=True))
if isinstance(x, tuple)
else _file_size(x, uncompressed=False)
for x in files
]
)
upload_kwargs = {
"metadata": appendables["valid_metadata"],
"tags": appendables["valid_tags"],
"project": project_id,
"coerce_ascii": coerce_ascii,
"progressbar": progressbar(length=total_size, label="Uploading..."),
}
run_via_threadpool(
ctx.obj["API"].Samples.upload,
files,
upload_kwargs,
max_threads=max_threads,
graceful_exit=False,
)
|
def upload(
ctx, files, max_threads, prompt, forward, reverse, tags, metadata, project_id, coerce_ascii
)
|
Upload a FASTA or FASTQ (optionally gzip'd) to One Codex
| 3.461039
| 3.404438
| 1.016626
|
base_url = os.environ.get("ONE_CODEX_API_BASE", "https://app.onecodex.com")
if not ctx.obj["API_KEY"]:
_login(base_url)
else:
email = _login(base_url, api_key=ctx.obj["API_KEY"])
ocx = Api(api_key=ctx.obj["API_KEY"], telemetry=ctx.obj["TELEMETRY"])
# TODO: This should be protected or built in as a first class resource
# with, e.g., connection error catching (it's not part of our formally documeted API at the moment)
if ocx._client.Account.instances()["email"] != email:
click.echo("Your login credentials do not match the provided email!", err=True)
_remove_creds()
ctx.exit(1)
|
def login(ctx)
|
Add an API key (saved in ~/.onecodex)
| 7.707067
| 6.668739
| 1.155701
|
tax_id_map = {}
if parent:
for row in classification.results()["table"]:
if row["parent_tax_id"] is not None and row["tax_id"] is not None:
tax_id_map[row["tax_id"]] = row["parent_tax_id"]
else:
for row in classification.results()["table"]:
if row["parent_tax_id"] is not None and row["tax_id"] is not None:
try:
tax_id_map[row["parent_tax_id"]].add(row["tax_id"])
except KeyError:
tax_id_map[row["parent_tax_id"]] = set([row["tax_id"]])
return tax_id_map
|
def make_taxonomy_dict(classification, parent=False)
|
Takes a classification data frame returned by the API and parses it
into a dictionary mapping a tax_id to its children (or parent).
Restricted to tax_id's that are represented in the classification
results.
| 1.826225
| 1.736982
| 1.051379
|
if parent:
# TODO: allow filtering on tax_id and its parents, too
pass
else:
def _child_recurse(tax_id, visited):
try:
children = [tax_id] + list(tax_id_map[tax_id])
except KeyError:
children = [tax_id]
for child in children:
if child not in visited:
visited.append(child)
children.extend(_child_recurse(child, visited))
return children
return list(set(_child_recurse(tax_id, [])))
|
def recurse_taxonomy_map(tax_id_map, tax_id, parent=False)
|
Takes the output dict from make_taxonomy_map and an input tax_id
and recurses either up or down through the tree to get /all/ children
(or parents) of the given tax_id.
| 3.165269
| 3.245358
| 0.975322
|
# FIXME more stable implementation that only attempts to resolve {"$ref"} objects where they are allowed.
if isinstance(schema, dict):
if len(schema) == 1 and "$ref" in schema and isinstance(schema["$ref"], six.string_types):
reference = schema["$ref"]
if reference.startswith("#"):
# TODO should also resolve any paths within the reference, which would need to be deferred.
return root
return ref_resolver(reference)
resolved = {}
for k, v in schema.items():
resolved[k] = schema_resolve_refs(v,
ref_resolver=ref_resolver,
root=root if root is not None else resolved)
return resolved
if isinstance(schema, (list, tuple)):
return [schema_resolve_refs(v, ref_resolver=ref_resolver, root=root) for v in schema]
return schema
|
def schema_resolve_refs(schema, ref_resolver=None, root=None)
|
Helper method for decoding references. Self-references are resolved automatically; other references are
resolved using a callback function.
:param object schema:
:param callable ref_resolver:
:param None root:
:return:
| 3.389351
| 3.38326
| 1.0018
|
cls = type(str(upper_camel_case(name)), (resource_cls or Resource, collections.MutableMapping), {
'__doc__': schema.get('description', '')
})
cls._schema = schema
cls._client = self
cls._links = links = {}
for link_schema in schema['links']:
link = Link(self,
rel=link_schema['rel'],
href=link_schema['href'],
method=link_schema['method'],
schema=link_schema.get('schema', None),
target_schema=link_schema.get('targetSchema', None))
# Set Resource._self, etc. for the special methods as they are managed by the Resource class
if link.rel in ('self', 'instances', 'create', 'update', 'destroy'):
setattr(cls, '_{}'.format(link.rel), link)
links[link.rel] = link
if link.rel != 'update': # 'update' is a special case because of MutableMapping.update()
setattr(cls, snake_case(link.rel), link)
# TODO routes (instance & non-instance)
for property_name, property_schema in schema.get('properties', {}).items():
# skip $uri and $id as these are already implemented in Resource and overriding them causes unnecessary
# fetches.
if property_name.startswith('$'):
continue
if property_schema.get('readOnly', False):
# TODO better error message. Raises AttributeError("can't set attribute")
setattr(cls,
property_name,
property(fget=partial((lambda name, obj: getitem(obj, name)), property_name),
doc=property_schema.get('description', None)))
else:
setattr(cls,
property_name,
property(fget=partial((lambda name, obj: getitem(obj, name)), property_name),
fset=partial((lambda name, obj, value: setitem(obj, name, value)), property_name),
fdel=partial((lambda name, obj: delitem(obj, name)), property_name),
doc=property_schema.get('description', None)))
root = None
if 'instances' in links:
root = cls._instances.href
elif 'self' in links:
root = cls._self.href[:cls._self.href.rfind('/')]
else:
root = self._root_path + '/' + name.replace('_', '-')
self._resources[root] = cls
return cls
|
def resource_factory(self, name, schema, resource_cls=None)
|
Registers a new resource with a given schema. The schema must not have any unresolved references
(such as `{"$ref": "#"}` for self-references, or otherwise). A subclass of :class:`Resource`
may be provided to add specific functionality to the resulting :class:`Resource`.
:param str name:
:param dict schema:
:param Resource resource_cls: a subclass of :class:`Resource` or None
:return: The new :class:`Resource`.
| 3.256697
| 3.370924
| 0.966114
|
result = []
for ib_file_path in find_files(directory, [".xib", ".storyboard"], exclude_dirs):
result += extract_string_pairs_in_ib_file(ib_file_path, special_ui_components_prefix)
return result
|
def extract_string_pairs_in_dir(directory, exclude_dirs, special_ui_components_prefix)
|
Extract string pairs in the given directory's xib/storyboard files.
Args:
directory (str): The path to the directory.
exclude_dirs (str): A list of directories to exclude from extraction.
special_ui_components_prefix (str):
If not None, extraction will not warn about internationalized UI components with this class prefix.
Returns:
list: The extracted string pairs for all IB files in the directory.
| 3.229626
| 2.587529
| 1.248151
|
element_entry_comment = get_element_attribute_or_empty(element, 'userLabel')
if element_entry_comment == "":
try:
element_entry_comment = element.getElementsByTagName('string')[0].firstChild.nodeValue
except Exception:
element_entry_comment = ""
if not element_entry_comment.lower().startswith(JT_INTERNATIONALIZED_COMMENT_PREFIX):
return None
else:
return element_entry_comment[len(JT_INTERNATIONALIZED_COMMENT_PREFIX):]
|
def extract_element_internationalized_comment(element)
|
Extracts the xib element's comment, if the element has been internationalized.
Args:
element (element): The element from which to extract the comment.
Returns:
The element's internationalized comment, None if it does not exist, or hasn't been internationalized (according
to the JTLocalize definitions).
| 3.255404
| 3.294518
| 0.988127
|
valid_class_names = ["%s%s" % (DEFAULT_UI_COMPONENTS_PREFIX, class_suffix)]
if special_ui_components_prefix is not None:
valid_class_names.append("%s%s" % (special_ui_components_prefix, class_suffix))
if (not element.hasAttribute('customClass')) or element.attributes['customClass'].value not in valid_class_names:
logging.warn("WARNING: %s is internationalized but isn't one of %s",
extract_element_internationalized_comment(element), valid_class_names)
|
def warn_if_element_not_of_class(element, class_suffix, special_ui_components_prefix)
|
Log a warning if the element is not of the given type (indicating that it is not internationalized).
Args:
element: The xib's XML element.
class_name: The type the element should be, but is missing.
special_ui_components_prefix: If provided, will not warn about class with this prefix (default is only 'JT')
| 3.579159
| 3.696615
| 0.968226
|
attributed_strings = ui_element.getElementsByTagName('attributedString')
if attributed_strings.length == 0:
return False
attributed_element = attributed_strings[0]
fragment_index = 1
for fragment in attributed_element.getElementsByTagName('fragment'):
# The fragment text is either as an attribute <fragment content="TEXT">
# or a child in the format <string key='content'>TEXT</string>
try:
label_entry_key = fragment.attributes['content'].value
except KeyError:
label_entry_key = fragment.getElementsByTagName('string')[0].firstChild.nodeValue
comment = "%s Part %d" % (comment_prefix, fragment_index)
results.append((label_entry_key, comment))
fragment_index += 1
return fragment_index > 1
|
def add_string_pairs_from_attributed_ui_element(results, ui_element, comment_prefix)
|
Adds string pairs from a UI element with attributed text
Args:
results (list): The list to add the results to.
attributed_element (element): The element from the xib that contains, to extract the fragments from.
comment_prefix (str): The prefix of the comment to use for extracted string
(will be appended "Part X" suffices)
Returns:
bool: Whether or not an attributed string was found.
| 4.06883
| 3.798327
| 1.071216
|
label_entry_comment = extract_element_internationalized_comment(label)
if label_entry_comment is None:
return
warn_if_element_not_of_class(label, 'Label', special_ui_components_prefix)
if label.hasAttribute('usesAttributedText') and label.attributes['usesAttributedText'].value == 'YES':
add_string_pairs_from_attributed_ui_element(results, label, label_entry_comment)
else:
try:
label_entry_key = label.attributes['text'].value
except KeyError:
try:
label_entry_key = label.getElementsByTagName('string')[0].firstChild.nodeValue
except Exception:
label_entry_key = 'N/A'
logging.warn("%s: Missing text entry in %s", xib_file, label.toxml('UTF8'))
results.append((label_entry_key, label_entry_comment))
|
def add_string_pairs_from_label_element(xib_file, results, label, special_ui_components_prefix)
|
Adds string pairs from a label element.
Args:
xib_file (str): Path to the xib file.
results (list): The list to add the results to.
label (element): The label element from the xib, to extract the string pairs from.
special_ui_components_prefix (str):
If not None, extraction will not warn about internationalized UI components with this class prefix.
| 3.578544
| 3.725979
| 0.960431
|
text_field_entry_comment = extract_element_internationalized_comment(text_field)
if text_field_entry_comment is None:
return
if text_field.hasAttribute('usesAttributedText') and text_field.attributes['usesAttributedText'].value == 'YES':
add_string_pairs_from_attributed_ui_element(results, text_field, text_field_entry_comment)
else:
try:
text_field_entry_key = text_field.attributes['text'].value
results.append((text_field_entry_key, text_field_entry_comment + ' default text value'))
except KeyError:
pass
try:
text_field_entry_key = text_field.attributes['placeholder'].value
results.append((text_field_entry_key, text_field_entry_comment + ' placeholder text value'))
except KeyError:
pass
warn_if_element_not_of_class(text_field, 'TextField', special_ui_components_prefix)
|
def add_string_pairs_from_text_field_element(xib_file, results, text_field, special_ui_components_prefix)
|
Adds string pairs from a textfield element.
Args:
xib_file (str): Path to the xib file.
results (list): The list to add the results to.
text_field(element): The textfield element from the xib, to extract the string pairs from.
special_ui_components_prefix (str):
If not None, extraction will not warn about internationalized UI components with this class prefix.
| 2.742346
| 2.847458
| 0.963085
|
text_view_entry_comment = extract_element_internationalized_comment(text_view)
if text_view_entry_comment is None:
return
if text_view.hasAttribute('usesAttributedText') and text_view.attributes['usesAttributedText'].value == 'YES':
add_string_pairs_from_attributed_ui_element(results, text_view, text_view_entry_comment)
else:
try:
text_view_entry_key = text_view.attributes['text'].value
results.append((text_view_entry_key, text_view_entry_comment + ' default text value'))
except KeyError:
pass
warn_if_element_not_of_class(text_view, 'TextView', special_ui_components_prefix)
|
def add_string_pairs_from_text_view_element(xib_file, results, text_view, special_ui_components_prefix)
|
Adds string pairs from a textview element.
Args:
xib_file (str): Path to the xib file.
results (list): The list to add the results to.
text_view(element): The textview element from the xib, to extract the string pairs from.
special_ui_components_prefix(str): A custom prefix for internationalize component to allow (default is only JT)
| 3.609712
| 3.804689
| 0.948753
|
button_entry_comment = extract_element_internationalized_comment(button)
if button_entry_comment is None:
return
for state in button.getElementsByTagName('state'):
state_name = state.attributes['key'].value
state_entry_comment = button_entry_comment + " - " + state_name + " state of button"
if not add_string_pairs_from_attributed_ui_element(results, state, state_entry_comment):
try:
button_entry_key = state.attributes['title'].value
except KeyError:
try:
button_entry_key = state.getElementsByTagName('string')[0].firstChild.nodeValue
except Exception:
continue
results.append((button_entry_key, state_entry_comment))
warn_if_element_not_of_class(button, 'Button', special_ui_components_prefix)
|
def add_string_pairs_from_button_element(xib_file, results, button, special_ui_components_prefix)
|
Adds strings pairs from a button xib element.
Args:
xib_file (str): Path to the xib file.
results (list): The list to add the results to.
button(element): The button element from the xib, to extract the string pairs from.
special_ui_components_prefix(str): A custom prefix for internationalize component to allow (default is only JT)
| 3.9053
| 4.196039
| 0.930711
|
try:
results = []
xmldoc = minidom.parse(file_path)
element_name_to_add_func = {'label': add_string_pairs_from_label_element,
'button': add_string_pairs_from_button_element,
'textField': add_string_pairs_from_text_field_element,
'textView': add_string_pairs_from_text_view_element}
for element_name in element_name_to_add_func:
add_func = element_name_to_add_func[element_name]
elements = xmldoc.getElementsByTagName(element_name)
for element in elements:
add_func(file_path, results, element, special_ui_components_prefix)
# Find strings of format JTL('Key Name', 'Key Comment') and add them to the results
jtl_brackets_find_results = re.findall(JTL_REGEX, open(file_path).read())
unescaped_jtl_brackets_find_results = [(unescape(x), unescape(y)) for (x, y) in jtl_brackets_find_results]
results += unescaped_jtl_brackets_find_results
if len(results) > 0:
results = [(None, os.path.basename(file_path))] + results
return results
except Exception, e:
logging.warn("ERROR: Error processing %s (%s: %s)", file_path, type(e), str(e))
return []
|
def extract_string_pairs_in_ib_file(file_path, special_ui_components_prefix)
|
Extract the strings pairs (key and comment) from a xib file.
Args:
file_path (str): The path to the xib file.
special_ui_components_prefix (str):
If not None, extraction will not warn about internationalized UI components with this class prefix.
Returns:
list: List of tuples representing the string pairs.
| 2.658982
| 2.649528
| 1.003568
|
old_translated_file_dictionary = generate_localization_key_to_entry_dictionary_from_file(translated_file)
if excluded_strings_file is not None and os.path.isfile(excluded_strings_file):
excluded_file_dictionary = generate_localization_key_to_entry_dictionary_from_file(excluded_strings_file)
else:
excluded_file_dictionary = {}
# The reason we keep a list of the keys, and not just pop is because values can repeat themselves.
translated_list = old_translated_file_dictionary.keys()
output_dictionary = {}
output_file_elements = []
f = open_strings_file(localizable_file, "r")
output_file_elements.append(Comment(u % (VALUE_PLACEHOLDER,)))
for _header_comment, comments, key, value in extract_header_comment_key_value_tuples_from_file(f):
if key in translated_list or key in excluded_file_dictionary:
if key in old_translated_file_dictionary:
old_translated_file_dictionary.pop(key)
elif value in output_dictionary:
output_dictionary[value].add_comments(comments)
output_file_elements.append(Comment(
u"/* There was a value '%s' here but it was a duplicate of an older value and removed. */\n" % value))
else:
loc_obj = LocalizationEntry(comments, value, VALUE_PLACEHOLDER)
output_dictionary[value] = loc_obj
output_file_elements.append(loc_obj)
for key, removed_trans in old_translated_file_dictionary.items():
output_file_elements.append(Comment(u % (", ".join(removed_trans.comments), removed_trans.key, removed_trans.value)))
write_file_elements_to_strings_file(output_translation_file, output_file_elements)
|
def localization_diff(localizable_file, translated_file, excluded_strings_file, output_translation_file)
|
Generates a strings file representing the strings that were yet to be translated.
Args:
localizable_file (str): The path to the localization strings file, meaning the file that represents the strings
that require translation.
translated_file (str): The path to the translated strings file, meaning the file containing the strings that
were already translated.
excluded_strings_file (str): The path to a file that contains all the strings we want to exclude from this and
from future diffs.
output_translation_file (str): The path to the output file, which will contain the strings the require
translation, but are not in the already given translation file.
| 3.694044
| 3.749312
| 0.985259
|
is_epub = isinstance(app.builder, EpubBuilder)
config_pages = app.config.html_additional_pages
if not is_epub and "404" not in config_pages:
yield ("404", {}, "404.html")
|
def add_404_page(app)
|
Build an extra ``404.html`` page if no ``"404"`` key is in the
``html_additional_pages`` config.
| 4.774262
| 3.561171
| 1.340644
|
base = context.get("canonical_url")
if not base:
return
target = app.builder.get_target_uri(pagename)
context["page_canonical_url"] = base + target
|
def canonical_url(app, pagename, templatename, context, doctree)
|
Build the canonical URL for a page. Appends the path for the
page to the base URL specified by the
``html_context["canonical_url"]`` config and stores it in
``html_context["page_canonical_url"]``.
| 4.430829
| 4.171243
| 1.062232
|
if app.config.singlehtml_sidebars is not None and isinstance(
app.builder, SingleFileHTMLBuilder
):
app.config.html_sidebars = app.config.singlehtml_sidebars
|
def singlehtml_sidebars(app)
|
When using a ``singlehtml`` builder, replace the
``html_sidebars`` config with ``singlehtml_sidebars``. This can be
used to change what sidebars are rendered for the single page called
``"index"`` by the builder.
| 4.263015
| 3.045997
| 1.399547
|
docstring = inspect.getdoc(obj) or ""
if skip or re.search(r"^\s*:internal:\s*$", docstring, re.M) is not None:
return True
|
def skip_internal(app, what, name, obj, skip, options)
|
Skip rendering autodoc when the docstring contains a line with
only the string `:internal:`.
| 4.668551
| 3.909586
| 1.194129
|
if what != "module":
return
lines[:] = [
line for line in lines if not line.startswith((":copyright:", ":license:"))
]
|
def cut_module_meta(app, what, name, obj, options, lines)
|
Don't render lines that start with ``:copyright:`` or
``:license:`` when rendering module autodoc. These lines are useful
meta information in the source code, but are noisy in the docs.
| 4.482841
| 3.200651
| 1.400603
|
try:
release = pkg_resources.get_distribution(name).version
except ImportError:
print(
textwrap.fill(
"'{name}' must be installed to build the documentation."
" Install from source using `pip install -e .` in a"
" virtualenv.".format(name=name)
)
)
sys.exit(1)
version = ".".join(release.split(".", version_length)[:version_length])
if placeholder:
version = "{}.{}".format(version, placeholder)
return release, version
|
def get_version(name, version_length=2, placeholder="x")
|
Ensures that the named package is installed and returns version
strings to be used by Sphinx.
Sphinx uses ``version`` to mean an abbreviated form of the full
version string, which is called ``release``. In ``conf.py``::
release, version = get_version("Flask")
# release = 1.0.x, version = 1.0.3.dev0
:param name: Name of package to get.
:param version_length: How many values from ``release`` to use for
``version``.
:param placeholder: Extra suffix to add to the version. The default
produces versions like ``1.2.x``.
:return: ``(release, version)`` tuple.
| 3.435224
| 3.129474
| 1.0977
|
if app.config.is_pallets_theme is not None:
return
theme = getattr(app.builder, "theme", None)
while theme is not None:
if theme.name == "pocoo":
app.config.is_pallets_theme = True
break
theme = theme.base
else:
app.config.is_pallets_theme = False
|
def set_is_pallets_theme(app)
|
Set the ``is_pallets_theme`` config to ``True`` if the current
theme is a decedent of the ``pocoo`` theme.
| 2.841461
| 2.36825
| 1.199815
|
def decorator(f):
@wraps(f)
def wrapped(app, *args, **kwargs):
if not app.config.is_pallets_theme:
return default
return f(app, *args, **kwargs)
return wrapped
return decorator
|
def only_pallets_theme(default=None)
|
Create a decorator that calls a function only if the
``is_pallets_theme`` config is ``True``.
Used to prevent Sphinx event callbacks from doing anything if the
Pallets themes are installed but not used. ::
@only_pallets_theme()
def inject_value(app):
...
app.connect("builder-inited", inject_value)
:param default: Value to return if a Pallets theme is not in use.
:return: A decorator.
| 2.909225
| 2.451757
| 1.186588
|
old_call = subprocess.call
def dummy_call(*args, **kwargs):
with tempfile.TemporaryFile("wb+") as f:
kwargs["stdout"] = f
kwargs["stderr"] = f
rv = subprocess.Popen(*args, **kwargs).wait()
f.seek(0)
click.echo(f.read().decode("utf-8", "replace").rstrip())
return rv
subprocess.call = dummy_call
try:
yield
finally:
subprocess.call = old_call
|
def patch_modules()
|
Patch modules to work better with :meth:`ExampleRunner.invoke`.
``subprocess.call` output is redirected to ``click.echo`` so it
shows up in the example output.
| 2.875278
| 2.564769
| 1.121067
|
runner = getattr(document, "click_example_runner", None)
if runner is None:
runner = document.click_example_runner = ExampleRunner()
return runner
|
def get_example_runner(document)
|
Get or create the :class:`ExampleRunner` instance associated with
a document.
| 3.671241
| 4.134465
| 0.88796
|
output_lines = _output_lines if _output_lines is not None else []
if env:
for key, value in sorted(env.items()):
value = shlex.quote(value)
output_lines.append("$ export {}={}".format(key, value))
args = args or []
if prog_name is None:
prog_name = cli.name.replace("_", "-")
output_lines.append(
"$ {} {}".format(prog_name, " ".join(shlex.quote(x) for x in args)).rstrip()
)
# remove "python" from command
prog_name = prog_name.rsplit(" ", 1)[-1]
if isinstance(input, (tuple, list)):
input = "\n".join(input) + "\n"
if terminate_input:
input += "\x04"
result = super(ExampleRunner, self).invoke(
cli=cli, args=args, input=input, env=env, prog_name=prog_name, **extra
)
output_lines.extend(result.output.splitlines())
return result
|
def invoke(
self,
cli,
args=None,
prog_name=None,
input=None,
terminate_input=False,
env=None,
_output_lines=None,
**extra
)
|
Like :meth:`CliRunner.invoke` but displays what the user
would enter in the terminal for env vars, command args, and
prompts.
:param terminate_input: Whether to display "^D" after a list of
input.
:param _output_lines: A list used internally to collect lines to
be displayed.
| 2.527381
| 2.503335
| 1.009606
|
with patch_modules():
code = compile(source, "<docs>", "exec")
exec(code, self.namespace)
|
def declare_example(self, source)
|
Execute the given code, adding it to the runner's namespace.
| 9.873701
| 8.115814
| 1.2166
|
code = compile(source, "<docs>", "exec")
buffer = []
invoke = partial(self.invoke, _output_lines=buffer)
def println(text=""):
buffer.append(text)
exec(
code,
self.namespace,
{
"invoke": invoke,
"println": println,
"isolated_filesystem": self.isolated_filesystem,
},
)
return buffer
|
def run_example(self, source)
|
Run commands by executing the given code, returning the lines
of input and output. The code should be a series of the
following functions:
* :meth:`invoke`: Invoke a command, adding env vars, input,
and output to the output.
* ``println(text="")``: Add a line of text to the output.
* :meth:`isolated_filesystem`: A context manager that changes
to a temporary directory while executing the block.
| 5.612088
| 4.468869
| 1.255819
|
_setup(verbose=verbose, quiet=quiet, color=color, title=title, timestamp=timestamp)
|
def setup(
*,
verbose: bool = False,
quiet: bool = False,
color: str = "auto",
title: str = "auto",
timestamp: bool = False
) -> None
|
Configure behavior of message functions.
:param verbose: Whether :func:`debug` messages should get printed
:param quiet: Hide every message except :func:`warning`, :func:`error`, and
:func:`fatal`
:param color: Choices: 'auto', 'always', or 'never'. Whether to color output.
By default ('auto'), only use color when output is a terminal.
:param title: Ditto for setting terminal title
:param timestamp: Whether to prefix every message with a time stamp
| 3.440093
| 4.160509
| 0.826844
|
# Flatten the list of tokens in case some of them are of
# class UnicodeSequence:
flat_tokens = list() # type: List[Token]
for token in tokens:
if isinstance(token, UnicodeSequence):
flat_tokens.extend(token.tuple())
else:
flat_tokens.append(token)
with_color = _process_tokens(flat_tokens, end=end, sep=sep, color=True)
without_color = _process_tokens(flat_tokens, end=end, sep=sep, color=False)
return (with_color, without_color)
|
def process_tokens(
tokens: Sequence[Token], *, end: str = "\n", sep: str = " "
) -> Tuple[str, str]
|
Returns two strings from a list of tokens.
One containing ASCII escape codes, the other
only the 'normal' characters
| 3.000441
| 2.838782
| 1.056947
|
if using_colorama():
global _INITIALIZED
if not _INITIALIZED:
colorama.init()
_INITIALIZED = True
with_color, without_color = process_tokens(tokens, end=end, sep=sep)
if CONFIG["record"]:
_MESSAGES.append(without_color)
if update_title and with_color:
write_title_string(without_color, fileobj)
to_write = with_color if config_color(fileobj) else without_color
write_and_flush(fileobj, to_write)
|
def message(
*tokens: Token,
end: str = "\n",
sep: str = " ",
fileobj: FileObj = sys.stdout,
update_title: bool = False
) -> None
|
Helper method for error, warning, info, debug
| 4.598363
| 4.391107
| 1.047199
|
error(*tokens, **kwargs)
sys.exit(1)
|
def fatal(*tokens: Token, **kwargs: Any) -> None
|
Print an error message and call ``sys.exit``
| 7.627457
| 4.602068
| 1.657398
|
tokens = [bold, red, "Error:"] + list(tokens) # type: ignore
kwargs["fileobj"] = sys.stderr
message(*tokens, **kwargs)
|
def error(*tokens: Token, **kwargs: Any) -> None
|
Print an error message
| 7.475709
| 6.000725
| 1.245801
|
tokens = [brown, "Warning:"] + list(tokens) # type: ignore
kwargs["fileobj"] = sys.stderr
message(*tokens, **kwargs)
|
def warning(*tokens: Token, **kwargs: Any) -> None
|
Print a warning message
| 8.527864
| 6.582118
| 1.295611
|
# We need to know the length of the section:
process_tokens_kwargs = kwargs.copy()
process_tokens_kwargs["color"] = False
no_color = _process_tokens(tokens, **process_tokens_kwargs)
info(*tokens, **kwargs)
info("-" * len(no_color), end="\n\n")
|
def info_section(*tokens: Token, **kwargs: Any) -> None
|
Print an underlined section name
| 5.603495
| 5.093201
| 1.100191
|
info(bold, blue, "::", reset, *tokens, **kwargs)
|
def info_1(*tokens: Token, **kwargs: Any) -> None
|
Print an important informative message
| 25.310633
| 14.629177
| 1.730147
|
end = "\n" if last else ""
info(".", end=end, fileobj=fileobj)
|
def dot(*, last: bool = False, fileobj: Any = None) -> None
|
Print a dot without a newline unless it is the last one.
Useful when you want to display a progress with very little
knowledge.
:param last: whether this is the last dot (will insert a newline)
| 8.582591
| 11.086362
| 0.774158
|
num_digits = len(str(n))
counter_format = "(%{}d/%d)".format(num_digits)
counter_str = counter_format % (i + 1, n)
info(green, "*", reset, counter_str, reset, *rest, **kwargs)
|
def info_count(i: int, n: int, *rest: Token, **kwargs: Any) -> None
|
Display a counter before the rest of the message.
``rest`` and ``kwargs`` are passed to :func:`info`
Current index should start at 0 and end at ``n-1``, like in ``enumerate()``
:param i: current index
:param n: total number of items
| 4.959136
| 5.148888
| 0.963147
|
if sys.stdout.isatty():
percent = float(value) / max_value * 100
sys.stdout.write(prefix + ": %.0f%%\r" % percent)
sys.stdout.flush()
|
def info_progress(prefix: str, value: float, max_value: float) -> None
|
Display info progress in percent.
:param value: the current value
:param max_value: the max value
:param prefix: the prefix message to print
| 3.001885
| 3.364559
| 0.892207
|
if not CONFIG["verbose"] or CONFIG["record"]:
return
message(*tokens, **kwargs)
|
def debug(*tokens: Token, **kwargs: Any) -> None
|
Print a debug message.
Messages are shown only when ``CONFIG["verbose"]`` is true
| 17.215492
| 12.202259
| 1.410845
|
return [" " * num + l for l in elems]
|
def indent_iterable(elems: Sequence[str], num: int = 2) -> List[str]
|
Indent an iterable.
| 7.078128
| 6.015532
| 1.176642
|
lines = text.splitlines()
return "\n".join(indent_iterable(lines, num=num))
|
def indent(text: str, num: int = 2) -> str
|
Indent a piece of text.
| 8.848722
| 5.800318
| 1.525558
|
tb = sys.exc_info()[2]
buffer = io.StringIO()
traceback.print_tb(tb, file=io) # type: ignore
# fmt: off
return (
red, message + "\n",
exception.__class__.__name__,
str(exception), "\n",
reset, buffer.getvalue()
)
|
def message_for_exception(exception: Exception, message: str) -> Sequence[Token]
|
Returns a tuple suitable for cli_ui.error()
from the given exception.
(Traceback will be part of the message, after
the ``message`` argument)
Useful when the exception occurs in an other thread
than the main one.
| 5.31242
| 5.007927
| 1.060802
|
tokens = get_ask_tokens(question)
if default:
tokens.append("(%s)" % default)
info(*tokens)
answer = read_input()
if not answer:
return default
return answer
|
def ask_string(*question: Token, default: Optional[str] = None) -> Optional[str]
|
Ask the user to enter a string.
| 4.962858
| 4.915463
| 1.009642
|
tokens = get_ask_tokens(question)
info(*tokens)
answer = read_password()
return answer
|
def ask_password(*question: Token) -> str
|
Ask the user to enter a password.
| 14.375617
| 11.099478
| 1.295162
|
if func_desc is None:
func_desc = lambda x: str(x)
tokens = get_ask_tokens(prompt)
info(*tokens)
choices.sort(key=func_desc)
for i, choice in enumerate(choices, start=1):
choice_desc = func_desc(choice)
info(" ", blue, "%i" % i, reset, choice_desc)
keep_asking = True
res = None
while keep_asking:
answer = read_input()
if not answer:
return None
try:
index = int(answer)
except ValueError:
info("Please enter a valid number")
continue
if index not in range(1, len(choices) + 1):
info(str(index), "is out of range")
continue
res = choices[index - 1]
keep_asking = False
return res
|
def ask_choice(
*prompt: Token, choices: List[Any], func_desc: Optional[FuncDesc] = None
) -> Any
|
Ask the user to choose from a list of choices.
:return: the selected choice
``func_desc`` will be called on every list item for displaying
and sorting the list. If not given, will default to
the identity function.
Will loop until:
* the user enters a valid index
* or leaves the prompt empty
In the last case, None will be returned
| 2.791514
| 2.890643
| 0.965707
|
while True:
tokens = [green, "::", reset] + list(question) + [reset]
if default:
tokens.append("(Y/n)")
else:
tokens.append("(y/N)")
info(*tokens)
answer = read_input()
if answer.lower() in ["y", "yes"]:
return True
if answer.lower() in ["n", "no"]:
return False
if not answer:
return default
warning("Please answer by 'y' (yes) or 'n' (no) ")
|
def ask_yes_no(*question: Token, default: bool = False) -> bool
|
Ask the user to answer by yes or no
| 3.562034
| 3.188222
| 1.117248
|
if not choices:
return message
else:
result = {
difflib.SequenceMatcher(a=user_input, b=choice).ratio(): choice
for choice in choices
}
message += "\nDid you mean: %s?" % result[max(result)]
return message
|
def did_you_mean(message: str, user_input: str, choices: Sequence[str]) -> str
|
Given a list of choices and an invalid user input, display the closest
items in the list that match the input.
| 3.466416
| 2.901819
| 1.194566
|
end_time = datetime.datetime.now()
elapsed_time = end_time - self.start_time
elapsed_seconds = elapsed_time.seconds
hours, remainder = divmod(int(elapsed_seconds), 3600)
minutes, seconds = divmod(remainder, 60)
as_str = "%sh %sm %ss %dms" % (
hours,
minutes,
seconds,
elapsed_time.microseconds / 1000,
)
info("%s took %s" % (self.description, as_str))
|
def stop(self) -> None
|
Stop the timer and emit a nice log
| 2.401627
| 2.194098
| 1.094585
|
parser = ET.XMLParser(resolve_entities=False, strip_cdata=False, remove_blank_text=True)
document = ET.fromstring(xml, parser)
return ('%s\n%s' % ('<?xml version="1.0" encoding="UTF-8"?>', ET.tostring(document, pretty_print=True).decode('utf-8'))).encode('utf-8')
|
def xmllint_format(xml)
|
Pretty-print XML like ``xmllint`` does.
Arguments:
xml (string): Serialized XML
| 2.05238
| 2.648992
| 0.774778
|
log = getLogger('ocrd.resolver.download_to_directory') # pylint: disable=redefined-outer-name
log.debug("directory=|%s| url=|%s| basename=|%s| overwrite=|%s| subdir=|%s|", directory, url, basename, overwrite, subdir)
if url is None:
raise Exception("'url' must be a string")
if directory is None:
raise Exception("'directory' must be a string")
if basename is None:
if (subdir is not None) or \
(directory and url.startswith('file://%s' % directory)): # in case downloading a url 'file:///tmp/foo/bar' to directory '/tmp/foo'
basename = url.rsplit('/', 1)[-1]
else:
basename = safe_filename(url)
if subdir is not None:
basename = join(subdir, basename)
outfilename = join(directory, basename)
if exists(outfilename) and not overwrite:
log.debug("File already exists and overwrite=False: %s", outfilename)
return outfilename
outfiledir = outfilename.rsplit('/', 1)[0]
# print(outfiledir)
if not isdir(outfiledir):
makedirs(outfiledir)
log.debug("Downloading <%s> to '%s'", url, outfilename)
# de-scheme file:// URL
if url.startswith('file://'):
url = url[len('file://'):]
# Copy files or download remote assets
if '://' not in url:
copyfile(url, outfilename)
else:
response = requests.get(url)
if response.status_code != 200:
raise Exception("Not found: %s (HTTP %d)" % (url, response.status_code))
with open(outfilename, 'wb') as outfile:
outfile.write(response.content)
return outfilename
|
def download_to_directory(self, directory, url, basename=None, overwrite=False, subdir=None)
|
Download a file to the workspace.
Early Shortcut: If url is a file://-URL and that file is already in the directory, keep it there.
If basename is not given but subdir is, assume user knows what she's doing and use last URL segment as the basename.
If basename is not given and no subdir is given, use the alnum characters in the URL as the basename.
Args:
directory (string): Directory to download files to
basename (string, None): basename part of the filename on disk.
url (string): URL to download from
overwrite (boolean): Whether to overwrite existing files with that name
subdir (string, None): Subdirectory to create within the directory. Think fileGrp.
Returns:
Local filename
| 2.76971
| 2.84056
| 0.975058
|
if dst_dir and not dst_dir.startswith('/'):
dst_dir = abspath(dst_dir)
if mets_url is None:
if baseurl is None:
raise Exception("Must pass mets_url and/or baseurl to workspace_from_url")
else:
mets_url = 'file://%s/%s' % (baseurl, mets_basename if mets_basename else 'mets.xml')
if baseurl is None:
baseurl = mets_url.rsplit('/', 1)[0]
log.debug("workspace_from_url\nmets_url='%s'\nbaseurl='%s'\ndst_dir='%s'", mets_url, baseurl, dst_dir)
# resolve to absolute
if '://' not in mets_url:
mets_url = 'file://%s' % abspath(mets_url)
if dst_dir is None:
# if mets_url is a file-url assume working directory is source directory
if mets_url.startswith('file://'):
# if dst_dir was not given and mets_url is a file assume that
# dst_dir should be the directory where the mets.xml resides
dst_dir = dirname(mets_url[len('file://'):])
else:
dst_dir = tempfile.mkdtemp(prefix=TMP_PREFIX)
log.debug("Creating workspace '%s' for METS @ <%s>", dst_dir, mets_url)
# if mets_basename is not given, use the last URL segment of the mets_url
if mets_basename is None:
mets_basename = mets_url \
.rsplit('/', 1)[-1] \
.split('?')[0] \
.split('#')[0]
dst_mets = join(dst_dir, mets_basename)
log.debug("Copying mets url '%s' to '%s'", mets_url, dst_mets)
if 'file://' + dst_mets == mets_url:
log.debug("Target and source mets are identical")
else:
if exists(dst_mets) and not clobber_mets:
raise Exception("File '%s' already exists but clobber_mets is false" % dst_mets)
else:
self.download_to_directory(dst_dir, mets_url, basename=mets_basename)
workspace = Workspace(self, dst_dir, mets_basename=mets_basename, baseurl=baseurl)
if download:
for f in workspace.mets.find_files():
workspace.download_file(f)
return workspace
|
def workspace_from_url(self, mets_url, dst_dir=None, clobber_mets=False, mets_basename=None, download=False, baseurl=None)
|
Create a workspace from a METS by URL.
Sets the mets.xml file
Arguments:
mets_url (string): Source mets URL
dst_dir (string, None): Target directory for the workspace
clobber_mets (boolean, False): Whether to overwrite existing mets.xml. By default existing mets.xml will raise an exception.
download (boolean, False): Whether to download all the files
baseurl (string, None): Base URL for resolving relative file locations
Returns:
Workspace
| 2.424286
| 2.47453
| 0.979696
|
if directory is None:
directory = tempfile.mkdtemp(prefix=TMP_PREFIX)
if not exists(directory):
makedirs(directory)
mets_fpath = join(directory, mets_basename)
if not clobber_mets and exists(mets_fpath):
raise Exception("Not clobbering existing mets.xml in '%s'." % directory)
mets = OcrdMets.empty_mets()
with open(mets_fpath, 'wb') as fmets:
log.info("Writing %s", mets_fpath)
fmets.write(mets.to_xml(xmllint=True))
return Workspace(self, directory, mets)
|
def workspace_from_nothing(self, directory, mets_basename='mets.xml', clobber_mets=False)
|
Create an empty workspace.
| 2.635131
| 2.549923
| 1.033416
|
root = self._tree.getroot()
ret = ET.tostring(ET.ElementTree(root), pretty_print=True)
if xmllint:
ret = xmllint_format(ret)
return ret
|
def to_xml(self, xmllint=False)
|
Serialize all properties as pretty-printed XML
Args:
xmllint (boolean): Format with ``xmllint`` in addition to pretty-printing
| 3.140363
| 3.737781
| 0.840168
|
ctx.obj = WorkspaceCtx(os.path.abspath(directory), mets_basename, automatic_backup=backup)
|
def workspace_cli(ctx, directory, mets_basename, backup)
|
Working with workspace
| 6.040464
| 5.859535
| 1.030878
|
workspace = ctx.resolver.workspace_from_url(
mets_url,
dst_dir=os.path.abspath(workspace_dir if workspace_dir else mkdtemp(prefix=TMP_PREFIX)),
mets_basename=ctx.mets_basename,
clobber_mets=clobber_mets,
download=download,
)
workspace.save_mets()
print(workspace.directory)
|
def workspace_clone(ctx, clobber_mets, download, mets_url, workspace_dir)
|
Create a workspace from a METS_URL and return the directory
METS_URL can be a URL, an absolute path or a path relative to $PWD.
If WORKSPACE_DIR is not provided, creates a temporary directory.
| 3.659447
| 3.697659
| 0.989666
|
workspace = ctx.resolver.workspace_from_nothing(
directory=os.path.abspath(directory),
mets_basename=ctx.mets_basename,
clobber_mets=clobber_mets
)
workspace.save_mets()
print(workspace.directory)
|
def workspace_create(ctx, clobber_mets, directory)
|
Create a workspace with an empty METS file in DIRECTORY.
Use '.' for $PWD"
| 4.091829
| 4.148216
| 0.986407
|
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