repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
onecodex/onecodex | onecodex/lib/upload.py | interleaved_filename | def interleaved_filename(file_path):
"""Return filename used to represent a set of paired-end files. Assumes Illumina-style naming
conventions where each file has _R1_ or _R2_ in its name."""
if not isinstance(file_path, tuple):
raise OneCodexException("Cannot get the interleaved filename without a ... | python | def interleaved_filename(file_path):
"""Return filename used to represent a set of paired-end files. Assumes Illumina-style naming
conventions where each file has _R1_ or _R2_ in its name."""
if not isinstance(file_path, tuple):
raise OneCodexException("Cannot get the interleaved filename without a ... | Return filename used to represent a set of paired-end files. Assumes Illumina-style naming
conventions where each file has _R1_ or _R2_ in its name. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L213-L222 |
onecodex/onecodex | onecodex/lib/upload.py | _file_size | def _file_size(file_path, uncompressed=False):
"""Return size of a single file, compressed or uncompressed"""
_, ext = os.path.splitext(file_path)
if uncompressed:
if ext in {".gz", ".gzip"}:
with gzip.GzipFile(file_path, mode="rb") as fp:
try:
fp.see... | python | def _file_size(file_path, uncompressed=False):
"""Return size of a single file, compressed or uncompressed"""
_, ext = os.path.splitext(file_path)
if uncompressed:
if ext in {".gz", ".gzip"}:
with gzip.GzipFile(file_path, mode="rb") as fp:
try:
fp.see... | Return size of a single file, compressed or uncompressed | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L225-L246 |
onecodex/onecodex | onecodex/lib/upload.py | _file_stats | def _file_stats(file_path, enforce_fastx=True):
"""Return information about the file path (or paths, if paired), prior to upload.
Parameters
----------
file_path : `string` or `tuple`
System path to the file(s) to be uploaded
Returns
-------
`string`
Filename, minus compres... | python | def _file_stats(file_path, enforce_fastx=True):
"""Return information about the file path (or paths, if paired), prior to upload.
Parameters
----------
file_path : `string` or `tuple`
System path to the file(s) to be uploaded
Returns
-------
`string`
Filename, minus compres... | Return information about the file path (or paths, if paired), prior to upload.
Parameters
----------
file_path : `string` or `tuple`
System path to the file(s) to be uploaded
Returns
-------
`string`
Filename, minus compressed extension (.gz or .bz2). If paired, use first path ... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L249-L309 |
onecodex/onecodex | onecodex/lib/upload.py | _call_init_upload | def _call_init_upload(file_name, file_size, metadata, tags, project, samples_resource):
"""Call init_upload at the One Codex API and return data used to upload the file.
Parameters
----------
file_name : `string`
The file_name you wish to associate this fastx file with at One Codex.
file_si... | python | def _call_init_upload(file_name, file_size, metadata, tags, project, samples_resource):
"""Call init_upload at the One Codex API and return data used to upload the file.
Parameters
----------
file_name : `string`
The file_name you wish to associate this fastx file with at One Codex.
file_si... | Call init_upload at the One Codex API and return data used to upload the file.
Parameters
----------
file_name : `string`
The file_name you wish to associate this fastx file with at One Codex.
file_size : `integer`
Accurate size of file to be uploaded, in bytes.
metadata : `dict`, o... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L334-L384 |
onecodex/onecodex | onecodex/lib/upload.py | _make_retry_fields | def _make_retry_fields(file_name, metadata, tags, project):
"""Generate fields to send to init_multipart_upload in the case that a Sample upload via
fastx-proxy fails.
Parameters
----------
file_name : `string`
The file_name you wish to associate this fastx file with at One Codex.
metad... | python | def _make_retry_fields(file_name, metadata, tags, project):
"""Generate fields to send to init_multipart_upload in the case that a Sample upload via
fastx-proxy fails.
Parameters
----------
file_name : `string`
The file_name you wish to associate this fastx file with at One Codex.
metad... | Generate fields to send to init_multipart_upload in the case that a Sample upload via
fastx-proxy fails.
Parameters
----------
file_name : `string`
The file_name you wish to associate this fastx file with at One Codex.
metadata : `dict`, optional
tags : `list`, optional
project : `s... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L387-L423 |
onecodex/onecodex | onecodex/lib/upload.py | upload_sequence | def upload_sequence(
files,
session,
samples_resource,
metadata=None,
tags=None,
project=None,
coerce_ascii=False,
progressbar=None,
):
"""Uploads a sequence file (or pair of files) to the One Codex server via either our proxy or directly to S3.
Parameters
----------
fil... | python | def upload_sequence(
files,
session,
samples_resource,
metadata=None,
tags=None,
project=None,
coerce_ascii=False,
progressbar=None,
):
"""Uploads a sequence file (or pair of files) to the One Codex server via either our proxy or directly to S3.
Parameters
----------
fil... | Uploads a sequence file (or pair of files) to the One Codex server via either our proxy or directly to S3.
Parameters
----------
files : `list`
A list of paths to files on the system, or tuples containing pairs of paths. Tuples will be
interleaved as paired-end reads and both files should c... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L426-L522 |
onecodex/onecodex | onecodex/lib/upload.py | _direct_upload | def _direct_upload(file_obj, file_name, fields, session, samples_resource):
"""Uploads a single file-like object via our validating proxy. Maintains compatibility with direct upload
to a user's S3 bucket as well in case we disable our validating proxy.
Parameters
----------
file_obj : `FASTXInterle... | python | def _direct_upload(file_obj, file_name, fields, session, samples_resource):
"""Uploads a single file-like object via our validating proxy. Maintains compatibility with direct upload
to a user's S3 bucket as well in case we disable our validating proxy.
Parameters
----------
file_obj : `FASTXInterle... | Uploads a single file-like object via our validating proxy. Maintains compatibility with direct upload
to a user's S3 bucket as well in case we disable our validating proxy.
Parameters
----------
file_obj : `FASTXInterleave`, `FilePassthru`, or a file-like object
A wrapper around a pair of fast... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L525-L623 |
onecodex/onecodex | onecodex/lib/upload.py | upload_sequence_fileobj | def upload_sequence_fileobj(file_obj, file_name, fields, retry_fields, session, samples_resource):
"""Uploads a single file-like object to the One Codex server via either fastx-proxy or directly
to S3.
Parameters
----------
file_obj : `FASTXInterleave`, `FilePassthru`, or a file-like object
... | python | def upload_sequence_fileobj(file_obj, file_name, fields, retry_fields, session, samples_resource):
"""Uploads a single file-like object to the One Codex server via either fastx-proxy or directly
to S3.
Parameters
----------
file_obj : `FASTXInterleave`, `FilePassthru`, or a file-like object
... | Uploads a single file-like object to the One Codex server via either fastx-proxy or directly
to S3.
Parameters
----------
file_obj : `FASTXInterleave`, `FilePassthru`, or a file-like object
A wrapper around a pair of fastx files (`FASTXInterleave`) or a single fastx file. In the
case of... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L626-L685 |
onecodex/onecodex | onecodex/lib/upload.py | upload_document | def upload_document(file_path, session, documents_resource, progressbar=None):
"""Uploads multiple document files to the One Codex server directly to S3 via an intermediate
bucket.
Parameters
----------
file_path : `str`
A path to a file on the system.
session : `requests.Session`
... | python | def upload_document(file_path, session, documents_resource, progressbar=None):
"""Uploads multiple document files to the One Codex server directly to S3 via an intermediate
bucket.
Parameters
----------
file_path : `str`
A path to a file on the system.
session : `requests.Session`
... | Uploads multiple document files to the One Codex server directly to S3 via an intermediate
bucket.
Parameters
----------
file_path : `str`
A path to a file on the system.
session : `requests.Session`
Connection to One Codex API.
documents_resource : `onecodex.models.Documents`
... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L688-L727 |
onecodex/onecodex | onecodex/lib/upload.py | upload_document_fileobj | def upload_document_fileobj(file_obj, file_name, session, documents_resource, log=None):
"""Uploads a single file-like object to the One Codex server directly to S3.
Parameters
----------
file_obj : `FilePassthru`, or a file-like object
If a file-like object is given, its mime-type will be sent... | python | def upload_document_fileobj(file_obj, file_name, session, documents_resource, log=None):
"""Uploads a single file-like object to the One Codex server directly to S3.
Parameters
----------
file_obj : `FilePassthru`, or a file-like object
If a file-like object is given, its mime-type will be sent... | Uploads a single file-like object to the One Codex server directly to S3.
Parameters
----------
file_obj : `FilePassthru`, or a file-like object
If a file-like object is given, its mime-type will be sent as 'text/plain'. Otherwise,
`FilePassthru` will send a compressed type if the file is g... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L730-L779 |
onecodex/onecodex | onecodex/lib/upload.py | _s3_intermediate_upload | def _s3_intermediate_upload(file_obj, file_name, fields, session, callback_url):
"""Uploads a single file-like object to an intermediate S3 bucket which One Codex can pull from
after receiving a callback.
Parameters
----------
file_obj : `FASTXInterleave`, `FilePassthru`, or a file-like object
... | python | def _s3_intermediate_upload(file_obj, file_name, fields, session, callback_url):
"""Uploads a single file-like object to an intermediate S3 bucket which One Codex can pull from
after receiving a callback.
Parameters
----------
file_obj : `FASTXInterleave`, `FilePassthru`, or a file-like object
... | Uploads a single file-like object to an intermediate S3 bucket which One Codex can pull from
after receiving a callback.
Parameters
----------
file_obj : `FASTXInterleave`, `FilePassthru`, or a file-like object
A wrapper around a pair of fastx files (`FASTXInterleave`) or a single fastx file. I... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L782-L861 |
onecodex/onecodex | onecodex/lib/upload.py | FASTXInterleave.seek | def seek(self, loc):
"""Called if upload fails and must be retried."""
assert loc == 0
# rewind progress bar
if self.progressbar:
self.progressbar.update(-self._tell)
self._fp_left.seek(loc)
self._fp_right.seek(loc)
self._tell = loc
self._buf... | python | def seek(self, loc):
"""Called if upload fails and must be retried."""
assert loc == 0
# rewind progress bar
if self.progressbar:
self.progressbar.update(-self._tell)
self._fp_left.seek(loc)
self._fp_right.seek(loc)
self._tell = loc
self._buf... | Called if upload fails and must be retried. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L140-L151 |
onecodex/onecodex | onecodex/lib/upload.py | FilePassthru.seek | def seek(self, loc):
"""Called if upload fails and must be retried."""
assert loc == 0
# rewind progress bar
if self.progressbar:
self.progressbar.update(-self._fp.tell())
self._fp.seek(loc) | python | def seek(self, loc):
"""Called if upload fails and must be retried."""
assert loc == 0
# rewind progress bar
if self.progressbar:
self.progressbar.update(-self._fp.tell())
self._fp.seek(loc) | Called if upload fails and must be retried. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/upload.py#L199-L207 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/merge_strings_files.py | merge_strings_files | def merge_strings_files(old_strings_file, new_strings_file):
""" Merges the old strings file with the new one.
Args:
old_strings_file (str): The path to the old strings file (previously produced, and possibly altered)
new_strings_file (str): The path to the new strings file (newly produced).
... | python | def merge_strings_files(old_strings_file, new_strings_file):
""" Merges the old strings file with the new one.
Args:
old_strings_file (str): The path to the old strings file (previously produced, and possibly altered)
new_strings_file (str): The path to the new strings file (newly produced).
... | Merges the old strings file with the new one.
Args:
old_strings_file (str): The path to the old strings file (previously produced, and possibly altered)
new_strings_file (str): The path to the new strings file (newly produced). | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/merge_strings_files.py#L24-L49 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_commandline_operation.py | LocalizationCommandLineOperation.configure_parser | def configure_parser(self, parser):
"""
Adds the necessary supported arguments to the argument parser.
Args:
parser (argparse.ArgumentParser): The parser to add arguments to.
"""
parser.add_argument("--log_path", default="", help="The log file path")
parser.a... | python | def configure_parser(self, parser):
"""
Adds the necessary supported arguments to the argument parser.
Args:
parser (argparse.ArgumentParser): The parser to add arguments to.
"""
parser.add_argument("--log_path", default="", help="The log file path")
parser.a... | Adds the necessary supported arguments to the argument parser.
Args:
parser (argparse.ArgumentParser): The parser to add arguments to. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_commandline_operation.py#L25-L33 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_commandline_operation.py | LocalizationCommandLineOperation.run_with_standalone_parser | def run_with_standalone_parser(self):
"""
Will run the operation as standalone with a new ArgumentParser
"""
parser = argparse.ArgumentParser(description=self.description())
self.configure_parser(parser)
self.run(parser.parse_args()) | python | def run_with_standalone_parser(self):
"""
Will run the operation as standalone with a new ArgumentParser
"""
parser = argparse.ArgumentParser(description=self.description())
self.configure_parser(parser)
self.run(parser.parse_args()) | Will run the operation as standalone with a new ArgumentParser | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_commandline_operation.py#L45-L51 |
onecodex/onecodex | onecodex/distance.py | DistanceMixin.alpha_diversity | def alpha_diversity(self, metric="simpson", rank="auto"):
"""Caculate the diversity within a community.
Parameters
----------
metric : {'simpson', 'chao1', 'shannon'}
The diversity metric to calculate.
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', ... | python | def alpha_diversity(self, metric="simpson", rank="auto"):
"""Caculate the diversity within a community.
Parameters
----------
metric : {'simpson', 'chao1', 'shannon'}
The diversity metric to calculate.
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', ... | Caculate the diversity within a community.
Parameters
----------
metric : {'simpson', 'chao1', 'shannon'}
The diversity metric to calculate.
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'}, optional
Analysis will be restricted... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/distance.py#L9-L42 |
onecodex/onecodex | onecodex/distance.py | DistanceMixin.beta_diversity | def beta_diversity(self, metric="braycurtis", rank="auto"):
"""Calculate the diversity between two communities.
Parameters
----------
metric : {'jaccard', 'braycurtis', 'cityblock'}
The distance metric to calculate.
rank : {'auto', 'kingdom', 'phylum', 'class', 'orde... | python | def beta_diversity(self, metric="braycurtis", rank="auto"):
"""Calculate the diversity between two communities.
Parameters
----------
metric : {'jaccard', 'braycurtis', 'cityblock'}
The distance metric to calculate.
rank : {'auto', 'kingdom', 'phylum', 'class', 'orde... | Calculate the diversity between two communities.
Parameters
----------
metric : {'jaccard', 'braycurtis', 'cityblock'}
The distance metric to calculate.
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'}, optional
Analysis will b... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/distance.py#L44-L73 |
onecodex/onecodex | onecodex/distance.py | DistanceMixin.unifrac | def unifrac(self, weighted=True, rank="auto"):
"""A beta diversity metric that takes into account the relative relatedness of community
members. Weighted UniFrac looks at abundances, unweighted UniFrac looks at presence.
Parameters
----------
weighted : `bool`
Calcul... | python | def unifrac(self, weighted=True, rank="auto"):
"""A beta diversity metric that takes into account the relative relatedness of community
members. Weighted UniFrac looks at abundances, unweighted UniFrac looks at presence.
Parameters
----------
weighted : `bool`
Calcul... | A beta diversity metric that takes into account the relative relatedness of community
members. Weighted UniFrac looks at abundances, unweighted UniFrac looks at presence.
Parameters
----------
weighted : `bool`
Calculate the weighted (True) or unweighted (False) distance met... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/distance.py#L75-L121 |
onecodex/onecodex | onecodex/lib/auth.py | fetch_api_key_from_uname | def fetch_api_key_from_uname(username, password, server_url):
"""
Retrieves an API key from the One Codex webpage given the username and password
"""
# TODO: Hit programmatic endpoint to fetch JWT key, not API key
with requests.Session() as session:
# get the login page normally
text... | python | def fetch_api_key_from_uname(username, password, server_url):
"""
Retrieves an API key from the One Codex webpage given the username and password
"""
# TODO: Hit programmatic endpoint to fetch JWT key, not API key
with requests.Session() as session:
# get the login page normally
text... | Retrieves an API key from the One Codex webpage given the username and password | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/auth.py#L16-L40 |
onecodex/onecodex | onecodex/lib/auth.py | check_version | def check_version(version, server):
"""Check if the current CLI version is supported by the One Codex backend.
Parameters
----------
version : `string`
Current version of the One Codex client library
server : `string`
Complete URL to One Codex server, e.g., https://app.onecodex.com
... | python | def check_version(version, server):
"""Check if the current CLI version is supported by the One Codex backend.
Parameters
----------
version : `string`
Current version of the One Codex client library
server : `string`
Complete URL to One Codex server, e.g., https://app.onecodex.com
... | Check if the current CLI version is supported by the One Codex backend.
Parameters
----------
version : `string`
Current version of the One Codex client library
server : `string`
Complete URL to One Codex server, e.g., https://app.onecodex.com
Returns
-------
`tuple` contai... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/lib/auth.py#L43-L88 |
onecodex/onecodex | onecodex/utils.py | valid_api_key | def valid_api_key(ctx, param, value):
"""
Ensures an API has valid length (this is a click callback)
"""
if value is not None and len(value) != 32:
raise click.BadParameter(
"API Key must be 32 characters long, not {}".format(str(len(value)))
)
else:
return value | python | def valid_api_key(ctx, param, value):
"""
Ensures an API has valid length (this is a click callback)
"""
if value is not None and len(value) != 32:
raise click.BadParameter(
"API Key must be 32 characters long, not {}".format(str(len(value)))
)
else:
return value | Ensures an API has valid length (this is a click callback) | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L100-L109 |
onecodex/onecodex | onecodex/utils.py | pprint | def pprint(j, no_pretty):
"""
Prints as formatted JSON
"""
if not no_pretty:
click.echo(
json.dumps(j, cls=PotionJSONEncoder, sort_keys=True, indent=4, separators=(",", ": "))
)
else:
click.echo(j) | python | def pprint(j, no_pretty):
"""
Prints as formatted JSON
"""
if not no_pretty:
click.echo(
json.dumps(j, cls=PotionJSONEncoder, sort_keys=True, indent=4, separators=(",", ": "))
)
else:
click.echo(j) | Prints as formatted JSON | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L112-L121 |
onecodex/onecodex | onecodex/utils.py | is_insecure_platform | def is_insecure_platform():
"""
Checks if the current system is missing an SSLContext object
"""
v = sys.version_info
if v.major == 3:
return False # Python 2 issue
if v.major == 2 and v.minor == 7 and v.micro >= 9:
return False # >= 2.7.9 includes the new SSL updates
try... | python | def is_insecure_platform():
"""
Checks if the current system is missing an SSLContext object
"""
v = sys.version_info
if v.major == 3:
return False # Python 2 issue
if v.major == 2 and v.minor == 7 and v.micro >= 9:
return False # >= 2.7.9 includes the new SSL updates
try... | Checks if the current system is missing an SSLContext object | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L188-L205 |
onecodex/onecodex | onecodex/utils.py | warn_if_insecure_platform | 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
"""
m = (
"\n"
"#################################################################################... | python | 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
"""
m = (
"\n"
"#################################################################################... | Produces a nice message if SSLContext object is not available.
Also returns True -> platform is insecure
False -> platform is secure | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L208-L233 |
onecodex/onecodex | onecodex/utils.py | download_file_helper | def download_file_helper(url, input_path):
"""
Manages the chunked downloading of a file given an url
"""
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)
... | python | def download_file_helper(url, input_path):
"""
Manages the chunked downloading of a file given an url
"""
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)
... | Manages the chunked downloading of a file given an url | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L245-L260 |
onecodex/onecodex | onecodex/utils.py | check_for_allowed_file | def check_for_allowed_file(f):
"""
Checks a file extension against a list of seq file exts
"""
for ext in SUPPORTED_EXTENSIONS:
if f.endswith(ext):
return True
log.error("Failed upload: Not an allowed file extension: %s", f)
raise SystemExit | python | def check_for_allowed_file(f):
"""
Checks a file extension against a list of seq file exts
"""
for ext in SUPPORTED_EXTENSIONS:
if f.endswith(ext):
return True
log.error("Failed upload: Not an allowed file extension: %s", f)
raise SystemExit | Checks a file extension against a list of seq file exts | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L263-L271 |
onecodex/onecodex | onecodex/utils.py | collapse_user | def collapse_user(fp):
"""
Converts a path back to ~/ from expanduser()
"""
home_dir = os.path.expanduser("~")
abs_path = os.path.abspath(fp)
return abs_path.replace(home_dir, "~") | python | def collapse_user(fp):
"""
Converts a path back to ~/ from expanduser()
"""
home_dir = os.path.expanduser("~")
abs_path = os.path.abspath(fp)
return abs_path.replace(home_dir, "~") | Converts a path back to ~/ from expanduser() | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L274-L280 |
onecodex/onecodex | onecodex/utils.py | telemetry | 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 dir... | python | 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 dir... | 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... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L353-L393 |
onecodex/onecodex | onecodex/utils.py | pretty_errors | 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.
"""
@wraps(fn)
def pretty_errors_wrapper(*args, **... | python | 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.
"""
@wraps(fn)
def pretty_errors_wrapper(*args, **... | 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. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L396-L413 |
onecodex/onecodex | onecodex/utils.py | atexit_unregister | def atexit_unregister(func, *args, **kwargs):
"""Python 2/3 compatible method for unregistering exit function.
Python2 has no atexit.unregister function :/
"""
try:
atexit.unregister(func, *args, **kwargs)
except AttributeError:
# This code runs in Python 2.7 *only*
# Only r... | python | def atexit_unregister(func, *args, **kwargs):
"""Python 2/3 compatible method for unregistering exit function.
Python2 has no atexit.unregister function :/
"""
try:
atexit.unregister(func, *args, **kwargs)
except AttributeError:
# This code runs in Python 2.7 *only*
# Only r... | Python 2/3 compatible method for unregistering exit function.
Python2 has no atexit.unregister function :/ | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/utils.py#L470-L483 |
onecodex/onecodex | onecodex/taxonomy.py | TaxonomyMixin.tree_build | 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... | python | 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... | 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. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/taxonomy.py#L5-L42 |
onecodex/onecodex | onecodex/taxonomy.py | TaxonomyMixin.tree_prune_tax_ids | 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 `li... | python | 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 `li... | 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.
Retur... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/taxonomy.py#L44-L68 |
onecodex/onecodex | onecodex/taxonomy.py | TaxonomyMixin.tree_prune_rank | 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 ... | python | 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 ... | 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', 'phy... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/taxonomy.py#L70-L106 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | write_file_elements_to_strings_file | 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.
"""
f = open_strings_file(file_path, "w")
for element in file_el... | python | 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.
"""
f = open_strings_file(file_path, "w")
for element in file_el... | 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. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L51-L63 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | setup_logging | def setup_logging(args=None):
""" Setup logging module.
Args:
args (optional): The arguments returned by the argparse module.
"""
logging_level = logging.WARNING
if args is not None and args.verbose:
logging_level = logging.INFO
config = {"level": logging_level, "format": "jtloc... | python | def setup_logging(args=None):
""" Setup logging module.
Args:
args (optional): The arguments returned by the argparse module.
"""
logging_level = logging.WARNING
if args is not None and args.verbose:
logging_level = logging.INFO
config = {"level": logging_level, "format": "jtloc... | Setup logging module.
Args:
args (optional): The arguments returned by the argparse module. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L66-L80 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | __generate_localization_dictionary_from_file | 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... | python | 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... | 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... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L83-L105 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | extract_header_comment_key_value_tuples_from_file | 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 localizat... | python | 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 localizat... | 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. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L132-L152 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | extract_jtl_string_pairs_from_text_file | 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 stri... | python | 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 stri... | 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 extra... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L155-L168 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | extract_string_pairs_in_directory | 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 localiza... | python | 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 localiza... | 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 paramet... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L171-L198 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | write_entry_to_file | 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.
"""
escaped_key = r... | python | 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.
"""
escaped_key = r... | 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. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L201-L211 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | append_dictionary_to_file | 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.... | python | 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.... | 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. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L224-L238 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | write_dict_to_new_file | 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.
"""
out... | python | 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.
"""
out... | 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. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L241-L253 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | find_files | 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 ... | python | 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 ... | 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 | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L256-L273 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_utils.py | should_include_file_in_search | 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 lis... | python | 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 lis... | 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 whet... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_utils.py#L276-L289 |
onecodex/onecodex | onecodex/analyses.py | AnalysisMixin._get_auto_rank | def _get_auto_rank(self, rank):
"""Tries to figure out what rank we should use for analyses"""
if rank == "auto":
# if we're an accessor for a ClassificationsDataFrame, use its _rank property
if self.__class__.__name__ == "OneCodexAccessor":
return self._rank
... | python | def _get_auto_rank(self, rank):
"""Tries to figure out what rank we should use for analyses"""
if rank == "auto":
# if we're an accessor for a ClassificationsDataFrame, use its _rank property
if self.__class__.__name__ == "OneCodexAccessor":
return self._rank
... | Tries to figure out what rank we should use for analyses | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/analyses.py#L27-L40 |
onecodex/onecodex | onecodex/analyses.py | AnalysisMixin._guess_normalized | 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... | python | 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... | 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. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/analyses.py#L42-L54 |
onecodex/onecodex | onecodex/analyses.py | AnalysisMixin._metadata_fetch | def _metadata_fetch(self, metadata_fields, label=None):
"""Takes a list of metadata fields, some of which can contain taxon names or taxon IDs, and
returns a DataFrame with transformed data that can be used for plotting.
Parameters
----------
metadata_fields : `list` of `string`... | python | def _metadata_fetch(self, metadata_fields, label=None):
"""Takes a list of metadata fields, some of which can contain taxon names or taxon IDs, and
returns a DataFrame with transformed data that can be used for plotting.
Parameters
----------
metadata_fields : `list` of `string`... | Takes a list of metadata fields, some of which can contain taxon names or taxon IDs, and
returns a DataFrame with transformed data that can be used for plotting.
Parameters
----------
metadata_fields : `list` of `string`
A list of metadata fields, taxon names, or taxon IDs t... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/analyses.py#L56-L224 |
onecodex/onecodex | onecodex/analyses.py | AnalysisMixin.to_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 ... | python | 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 ... | 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
Analy... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/analyses.py#L226-L329 |
onecodex/onecodex | onecodex/notebooks/exporters.py | OneCodexHTMLExporter.from_notebook_node | def from_notebook_node(self, nb, resources=None, **kw):
"""Uses nbconvert's HTMLExporter to generate HTML, with slight modifications.
Notes
-----
This exporter will only save cells generated with Altair/Vega if they have an SVG image type
stored with them. This data is only stor... | python | def from_notebook_node(self, nb, resources=None, **kw):
"""Uses nbconvert's HTMLExporter to generate HTML, with slight modifications.
Notes
-----
This exporter will only save cells generated with Altair/Vega if they have an SVG image type
stored with them. This data is only stor... | Uses nbconvert's HTMLExporter to generate HTML, with slight modifications.
Notes
-----
This exporter will only save cells generated with Altair/Vega if they have an SVG image type
stored with them. This data is only stored if our fork of `ipyvega` is installed or the onecodex
# ... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/notebooks/exporters.py#L42-L145 |
onecodex/onecodex | onecodex/notebooks/exporters.py | OneCodexPDFExporter.from_notebook_node | def from_notebook_node(self, nb, resources=None, **kw):
"""Takes output of OneCodexHTMLExporter and runs Weasyprint to get a PDF."""
from weasyprint import HTML, CSS
nb = copy.deepcopy(nb)
output, resources = super(OneCodexPDFExporter, self).from_notebook_node(
nb, resource... | python | def from_notebook_node(self, nb, resources=None, **kw):
"""Takes output of OneCodexHTMLExporter and runs Weasyprint to get a PDF."""
from weasyprint import HTML, CSS
nb = copy.deepcopy(nb)
output, resources = super(OneCodexPDFExporter, self).from_notebook_node(
nb, resource... | Takes output of OneCodexHTMLExporter and runs Weasyprint to get a PDF. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/notebooks/exporters.py#L160-L174 |
onecodex/onecodex | onecodex/notebooks/exporters.py | OneCodexDocumentExporter.from_notebook_node | def from_notebook_node(self, nb, resources=None, **kw):
"""Takes PDF output from PDFExporter and uploads to One Codex Documents portal."""
output, resources = super(OneCodexDocumentExporter, self).from_notebook_node(
nb, resources=resources, **kw
)
from onecodex import Api
... | python | def from_notebook_node(self, nb, resources=None, **kw):
"""Takes PDF output from PDFExporter and uploads to One Codex Documents portal."""
output, resources = super(OneCodexDocumentExporter, self).from_notebook_node(
nb, resources=resources, **kw
)
from onecodex import Api
... | Takes PDF output from PDFExporter and uploads to One Codex Documents portal. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/notebooks/exporters.py#L185-L219 |
joytunes/JTLocalize | localization_flow/jtlocalize/genstrings.py | generate_strings | 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 i... | python | 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 i... | 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. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/genstrings.py#L64-L122 |
onecodex/onecodex | onecodex/models/collection.py | SampleCollection.filter | 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
--------... | python | 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
--------... | 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`
... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/models/collection.py#L89-L117 |
onecodex/onecodex | onecodex/models/collection.py | SampleCollection._classification_fetch | 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 go... | python | 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 go... | 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... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/models/collection.py#L123-L156 |
onecodex/onecodex | onecodex/models/collection.py | SampleCollection._collate_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.
"""
import pandas as pd
DEFAULT_FIELDS = None
metadata = []
... | python | 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.
"""
import pandas as pd
DEFAULT_FIELDS = None
metadata = []
... | Turns a list of objects associated with a classification result into a DataFrame of
metadata.
Returns
-------
None, but stores a result in self._cached. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/models/collection.py#L165-L203 |
onecodex/onecodex | onecodex/models/collection.py | SampleCollection._collate_results | 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 ... | python | 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 ... | 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 samp... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/models/collection.py#L212-L271 |
onecodex/onecodex | onecodex/models/collection.py | SampleCollection.to_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.
R... | python | 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.
R... | 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 : ... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/models/collection.py#L294-L371 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_merge_back.py | localization_merge_back | 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
... | python | 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
... | 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 transl... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_merge_back.py#L28-L62 |
onecodex/onecodex | onecodex/viz/_primitives.py | boxplot | 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 o... | python | 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 o... | 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 n... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/viz/_primitives.py#L7-L71 |
onecodex/onecodex | onecodex/viz/_primitives.py | dendrogram | 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... | python | 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... | 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 t... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/viz/_primitives.py#L74-L117 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/add_genstrings_comments_to_file.py | add_genstrings_comments_to_file | 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.
"""
errors_to_log = [line for line in genstrings_err.splitlines() if "used with mult... | python | 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.
"""
errors_to_log = [line for line in genstrings_err.splitlines() if "used with mult... | Adds the comments produced by the genstrings script for duplicate keys.
Args:
localization_file (str): The path to the strings file. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/add_genstrings_comments_to_file.py#L26-L57 |
onecodex/onecodex | onecodex/viz/_distance.py | VizDistanceMixin.plot_distance | def plot_distance(
self,
rank="auto",
metric="braycurtis",
title=None,
xlabel=None,
ylabel=None,
tooltip=None,
return_chart=False,
linkage="average",
label=None,
):
"""Plot beta diversity distance matrix as a heatmap and dendrog... | python | def plot_distance(
self,
rank="auto",
metric="braycurtis",
title=None,
xlabel=None,
ylabel=None,
tooltip=None,
return_chart=False,
linkage="average",
label=None,
):
"""Plot beta diversity distance matrix as a heatmap and dendrog... | Plot beta diversity distance matrix as a heatmap and dendrogram.
Parameters
----------
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'}, optional
Analysis will be restricted to abundances of taxa at the specified level.
metric : {'braycurt... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/viz/_distance.py#L76-L201 |
onecodex/onecodex | onecodex/viz/_distance.py | VizDistanceMixin.plot_mds | def plot_mds(
self,
rank="auto",
metric="braycurtis",
method="pcoa",
title=None,
xlabel=None,
ylabel=None,
color=None,
size=None,
tooltip=None,
return_chart=False,
label=None,
):
"""Plot beta diversity distance m... | python | def plot_mds(
self,
rank="auto",
metric="braycurtis",
method="pcoa",
title=None,
xlabel=None,
ylabel=None,
color=None,
size=None,
tooltip=None,
return_chart=False,
label=None,
):
"""Plot beta diversity distance m... | Plot beta diversity distance matrix using multidimensional scaling (MDS).
Parameters
----------
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'}, optional
Analysis will be restricted to abundances of taxa at the specified level.
metric : {... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/viz/_distance.py#L203-L371 |
onecodex/onecodex | onecodex/models/helpers.py | ResourceDownloadMixin.download | 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.
... | python | 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.
... | 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 f... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/models/helpers.py#L93-L159 |
onecodex/onecodex | onecodex/models/misc.py | Documents.upload | 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 us... | python | 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 us... | 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 `Sa... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/models/misc.py#L58-L75 |
joytunes/JTLocalize | localization_flow/jtlocalize/prepare_for_translation.py | prepare_for_translation | 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_pat... | python | 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_pat... | 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. | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/prepare_for_translation.py#L31-L60 |
onecodex/onecodex | onecodex/cli.py | onecodex | def onecodex(ctx, api_key, no_pprint, verbose, telemetry):
"""One Codex v1 API command line interface"""
# 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"] = tel... | python | def onecodex(ctx, api_key, no_pprint, verbose, telemetry):
"""One Codex v1 API command line interface"""
# 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"] = tel... | One Codex v1 API command line interface | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/cli.py#L68-L82 |
onecodex/onecodex | onecodex/cli.py | documents_upload | def documents_upload(ctx, max_threads, files):
"""Upload a document file (of any type) to One Codex"""
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_thread... | python | def documents_upload(ctx, max_threads, files):
"""Upload a document file (of any type) to One Codex"""
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_thread... | Upload a document file (of any type) to One Codex | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/cli.py#L176-L191 |
onecodex/onecodex | onecodex/cli.py | classifications | def classifications(ctx, classifications, results, readlevel, readlevel_path):
"""Retrieve performed metagenomic classifications"""
# basic operation -- just print
if not readlevel and not results:
cli_resource_fetcher(ctx, "classifications", classifications)
# fetch the results
elif not r... | python | def classifications(ctx, classifications, results, readlevel, readlevel_path):
"""Retrieve performed metagenomic classifications"""
# basic operation -- just print
if not readlevel and not results:
cli_resource_fetcher(ctx, "classifications", classifications)
# fetch the results
elif not r... | Retrieve performed metagenomic classifications | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/cli.py#L252-L290 |
onecodex/onecodex | onecodex/cli.py | upload | 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"""
appendables = {}
if tags:
appendables["tags"] = []
for tag in tags:
appendables["tags"].append(tag)
... | python | 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"""
appendables = {}
if tags:
appendables["tags"] = []
for tag in tags:
appendables["tags"].append(tag)
... | Upload a FASTA or FASTQ (optionally gzip'd) to One Codex | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/cli.py#L333-L439 |
onecodex/onecodex | onecodex/cli.py | login | def login(ctx):
"""Add an API key (saved in ~/.onecodex)"""
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"], tel... | python | def login(ctx):
"""Add an API key (saved in ~/.onecodex)"""
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"], tel... | Add an API key (saved in ~/.onecodex) | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/cli.py#L445-L459 |
onecodex/onecodex | onecodex/scripts/subset_reads.py | make_taxonomy_dict | 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.
"""
tax_id_map = {}
i... | python | 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.
"""
tax_id_map = {}
i... | 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. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/scripts/subset_reads.py#L63-L85 |
onecodex/onecodex | onecodex/scripts/subset_reads.py | recurse_taxonomy_map | 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.
"""
if parent:
# TODO: allow filtering on tax_id and i... | python | 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.
"""
if parent:
# TODO: allow filtering on tax_id and i... | 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. | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/scripts/subset_reads.py#L88-L113 |
onecodex/onecodex | onecodex/vendored/potion_client/converter.py | schema_resolve_refs | 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:
"... | python | 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:
"... | 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: | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/vendored/potion_client/converter.py#L153-L180 |
onecodex/onecodex | onecodex/notebooks/report.py | reference | def reference(text=None, label=None):
"""Add a reference to the bibliography and insert a superscript number.
Parameters
----------
text : `string`, optional
The complete text of the reference, e.g. Roo, et al. "How to Python." Nature, 2019.
label : `string`, optional
A short label ... | python | def reference(text=None, label=None):
"""Add a reference to the bibliography and insert a superscript number.
Parameters
----------
text : `string`, optional
The complete text of the reference, e.g. Roo, et al. "How to Python." Nature, 2019.
label : `string`, optional
A short label ... | Add a reference to the bibliography and insert a superscript number.
Parameters
----------
text : `string`, optional
The complete text of the reference, e.g. Roo, et al. "How to Python." Nature, 2019.
label : `string`, optional
A short label to describe this reference.
Notes
--... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/notebooks/report.py#L211-L314 |
onecodex/onecodex | onecodex/vendored/potion_client/__init__.py | Client.resource_factory | 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 `{"$ref": "#"}` for self-references, or otherwise). A subclass of :class:`Resource`
may be provided to add specific f... | python | def resource_factory(self, name, schema, resource_cls=None):
"""
Registers a new resource with a given schema. The schema must not have any unresolved references
(such as `{"$ref": "#"}` for self-references, or otherwise). A subclass of :class:`Resource`
may be provided to add specific f... | 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:
... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/vendored/potion_client/__init__.py#L78-L144 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | extract_string_pairs_in_dir | 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... | python | 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... | 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 internation... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L32-L49 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | extract_element_internationalized_comment | 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... | python | 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... | 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 JTLocal... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L66-L86 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | warn_if_element_not_of_class | 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.
... | python | 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.
... | 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 (defau... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L89-L103 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | add_string_pairs_from_attributed_ui_element | 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... | python | 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... | 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
... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L106-L136 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | add_string_pairs_from_label_element | 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 ex... | python | 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 ex... | 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, extract... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L139-L167 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | add_string_pairs_from_text_field_element | 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 eleme... | python | 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 eleme... | 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 N... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L170-L198 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | add_string_pairs_from_text_view_element | 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 fr... | python | 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 fr... | 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 inte... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L201-L223 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | add_string_pairs_from_button_element | 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 x... | python | 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 x... | 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 intern... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L226-L254 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py | extract_string_pairs_in_ib_file | 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 internation... | python | 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 internation... | 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 tuple... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/create_localized_strings_from_ib_files.py#L257-L295 |
joytunes/JTLocalize | localization_flow/jtlocalize/core/localization_diff.py | localization_diff | 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 s... | python | 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 s... | 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 fil... | https://github.com/joytunes/JTLocalize/blob/87864dc60114e0e61c768d057c6eddfadff3f40a/localization_flow/jtlocalize/core/localization_diff.py#L32-L88 |
onecodex/onecodex | onecodex/viz/_metadata.py | VizMetadataMixin.plot_metadata | def plot_metadata(
self,
rank="auto",
haxis="Label",
vaxis="simpson",
title=None,
xlabel=None,
ylabel=None,
return_chart=False,
plot_type="auto",
label=None,
):
"""Plot an arbitrary metadata field versus an arbitrary quantity as... | python | def plot_metadata(
self,
rank="auto",
haxis="Label",
vaxis="simpson",
title=None,
xlabel=None,
ylabel=None,
return_chart=False,
plot_type="auto",
label=None,
):
"""Plot an arbitrary metadata field versus an arbitrary quantity as... | Plot an arbitrary metadata field versus an arbitrary quantity as a boxplot or scatter plot.
Parameters
----------
rank : {'auto', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species'}, optional
Analysis will be restricted to abundances of taxa at the specified level.
... | https://github.com/onecodex/onecodex/blob/326a0a1af140e3a57ccf31c3c9c5e17a5775c13d/onecodex/viz/_metadata.py#L9-L175 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/__init__.py | add_404_page | def add_404_page(app):
"""Build an extra ``404.html`` page if no ``"404"`` key is in the
``html_additional_pages`` config.
"""
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", {}, "... | python | def add_404_page(app):
"""Build an extra ``404.html`` page if no ``"404"`` key is in the
``html_additional_pages`` config.
"""
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", {}, "... | Build an extra ``404.html`` page if no ``"404"`` key is in the
``html_additional_pages`` config. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/__init__.py#L52-L60 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/__init__.py | canonical_url | 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"]``.
"""
base = context.get("canoni... | python | 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"]``.
"""
base = context.get("canoni... | 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"]``. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/__init__.py#L64-L76 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/__init__.py | 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.
"""
if app.config.singlehtml_sidebars is not None ... | python | 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.
"""
if app.config.singlehtml_sidebars is not None ... | 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. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/__init__.py#L80-L89 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/__init__.py | skip_internal | def skip_internal(app, what, name, obj, skip, options):
"""Skip rendering autodoc when the docstring contains a line with
only the string `:internal:`.
"""
docstring = inspect.getdoc(obj) or ""
if skip or re.search(r"^\s*:internal:\s*$", docstring, re.M) is not None:
return True | python | def skip_internal(app, what, name, obj, skip, options):
"""Skip rendering autodoc when the docstring contains a line with
only the string `:internal:`.
"""
docstring = inspect.getdoc(obj) or ""
if skip or re.search(r"^\s*:internal:\s*$", docstring, re.M) is not None:
return True | Skip rendering autodoc when the docstring contains a line with
only the string `:internal:`. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/__init__.py#L93-L100 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/__init__.py | cut_module_meta | 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.
"""
if what != "module":
return
lines[:... | python | 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.
"""
if what != "module":
return
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. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/__init__.py#L104-L114 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/__init__.py | get_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, vers... | python | 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, vers... | 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... | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/__init__.py#L117-L151 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/theme_check.py | set_is_pallets_theme | 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.
"""
if app.config.is_pallets_theme is not None:
return
theme = getattr(app.builder, "theme", None)
while theme is not None:
if theme.name... | python | 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.
"""
if app.config.is_pallets_theme is not None:
return
theme = getattr(app.builder, "theme", None)
while theme is not None:
if theme.name... | Set the ``is_pallets_theme`` config to ``True`` if the current
theme is a decedent of the ``pocoo`` theme. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/theme_check.py#L4-L20 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/theme_check.py | only_pallets_theme | 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(... | python | 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(... | 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("b... | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/theme_check.py#L23-L50 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/themes/click/domain.py | patch_modules | 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.
"""
old_call = subprocess.call
def dummy_call(*args, **kwargs):
with tempfile.TemporaryFile("wb+") as ... | python | 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.
"""
old_call = subprocess.call
def dummy_call(*args, **kwargs):
with tempfile.TemporaryFile("wb+") as ... | 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. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/themes/click/domain.py#L62-L84 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/themes/click/domain.py | get_example_runner | def get_example_runner(document):
"""Get or create the :class:`ExampleRunner` instance associated with
a document.
"""
runner = getattr(document, "click_example_runner", None)
if runner is None:
runner = document.click_example_runner = ExampleRunner()
return runner | python | def get_example_runner(document):
"""Get or create the :class:`ExampleRunner` instance associated with
a document.
"""
runner = getattr(document, "click_example_runner", None)
if runner is None:
runner = document.click_example_runner = ExampleRunner()
return runner | Get or create the :class:`ExampleRunner` instance associated with
a document. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/themes/click/domain.py#L199-L206 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/themes/click/domain.py | ExampleRunner.invoke | 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, ... | python | 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, ... | 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
b... | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/themes/click/domain.py#L109-L157 |
pallets/pallets-sphinx-themes | src/pallets_sphinx_themes/themes/click/domain.py | ExampleRunner.declare_example | def declare_example(self, source):
"""Execute the given code, adding it to the runner's namespace."""
with patch_modules():
code = compile(source, "<docs>", "exec")
exec(code, self.namespace) | python | def declare_example(self, source):
"""Execute the given code, adding it to the runner's namespace."""
with patch_modules():
code = compile(source, "<docs>", "exec")
exec(code, self.namespace) | Execute the given code, adding it to the runner's namespace. | https://github.com/pallets/pallets-sphinx-themes/blob/1d4517d76dd492017f17acd7f72e82e40a1f1bc6/src/pallets_sphinx_themes/themes/click/domain.py#L159-L163 |
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