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def _list_patient_ids(self):
""" Utility function to return a list of patient ids in the Cohort """ |
results = []
for patient in self:
results.append(patient.id)
return(results) |
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def summarize_provenance_per_cache(self):
"""Utility function to summarize provenance files for cached items used by a Cohort, for each cache_dir that exists. On... |
provenance_summary = {}
df = self.as_dataframe()
for cache in self.cache_names:
cache_name = self.cache_names[cache]
cache_provenance = None
num_discrepant = 0
this_cache_dir = path.join(self.cache_dir, cache_name)
if path.exists(this_... |
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def summarize_provenance(self):
"""Utility function to summarize provenance files for cached items used by a Cohort. At the moment, most PROVENANCE files contain... |
provenance_per_cache = self.summarize_provenance_per_cache()
summary_provenance = None
num_discrepant = 0
for cache in provenance_per_cache:
if not(summary_provenance):
## pick arbitrary provenance & call this the "summary" (for now)
summary_p... |
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def summarize_data_sources(self):
"""Utility function to summarize data source status for this Cohort, useful for confirming the state of data used for an analys... |
provenance_file_summary = self.summarize_provenance()
dataframe_hash = self.summarize_dataframe()
results = {
"provenance_file_summary": provenance_file_summary,
"dataframe_hash": dataframe_hash
}
return(results) |
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def strelka_somatic_variant_stats(variant, variant_metadata):
"""Parse out the variant calling statistics for a given variant from a Strelka VCF Parameters varia... |
sample_info = variant_metadata["sample_info"]
# Ensure there are exactly two samples in the VCF, a tumor and normal
assert len(sample_info) == 2, "More than two samples found in the somatic VCF"
tumor_stats = _strelka_variant_stats(variant, sample_info["TUMOR"])
normal_stats = _strelka_variant_sta... |
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def _strelka_variant_stats(variant, sample_info):
"""Parse a single sample"s variant calling statistics based on Strelka VCF output Parameters variant : varcode.... |
if variant.is_deletion or variant.is_insertion:
# ref: https://sites.google.com/site/strelkasomaticvariantcaller/home/somatic-variant-output
ref_depth = int(sample_info['TAR'][0]) # number of reads supporting ref allele (non-deletion)
alt_depth = int(sample_info['TIR'][0]) # number of ... |
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def mutect_somatic_variant_stats(variant, variant_metadata):
"""Parse out the variant calling statistics for a given variant from a Mutect VCF Parameters variant... |
sample_info = variant_metadata["sample_info"]
# Ensure there are exactly two samples in the VCF, a tumor and normal
assert len(sample_info) == 2, "More than two samples found in the somatic VCF"
# Find the sample with the genotype field set to variant in the VCF
tumor_sample_infos = [info for inf... |
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def maf_somatic_variant_stats(variant, variant_metadata):
""" Parse out the variant calling statistics for a given variant from a MAF file Assumes the MAF format... |
tumor_stats = None
normal_stats = None
if "t_ref_count" in variant_metadata:
tumor_stats = _maf_variant_stats(variant, variant_metadata, prefix="t")
if "n_ref_count" in variant_metadata:
normal_stats = _maf_variant_stats(variant, variant_metadata, prefix="n")
return SomaticVariantSt... |
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def _vcf_is_strelka(variant_file, variant_metadata):
"""Return True if variant_file given is in strelka format """ |
if "strelka" in variant_file.lower():
return True
elif "NORMAL" in variant_metadata["sample_info"].keys():
return True
else:
vcf_reader = vcf.Reader(open(variant_file, "r"))
try:
vcf_type = vcf_reader.metadata["content"]
except KeyError:
vcf_t... |
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def variant_stats_from_variant(variant, metadata, merge_fn=(lambda all_stats: \ max(all_stats, key=(lambda stats: stats.tumor_stats.depth)))):
"""Parse the varia... |
all_stats = []
for (variant_file, variant_metadata) in metadata.items():
if _vcf_is_maf(variant_file=variant_file):
stats = maf_somatic_variant_stats(variant, variant_metadata)
elif _vcf_is_strelka(variant_file=variant_file,
variant_metadata=variant_meta... |
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def load_ensembl_coverage(cohort, coverage_path, min_tumor_depth, min_normal_depth=0, pageant_dir_fn=None):
""" Load in Pageant CoverageDepth results with Ensemb... |
# Function to grab the pageant file name using the Patient
if pageant_dir_fn is None:
pageant_dir_fn = lambda patient: patient.id
columns_both = [
"depth1", # Normal
"depth2", # Tumor
"onBP1",
"onBP2",
"numOnLoci",
"fracBPOn1",
"fracBPOn2",
... |
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def vertical_percent(plot, percent=0.1):
""" Using the size of the y axis, return a fraction of that size. """ |
plot_bottom, plot_top = plot.get_ylim()
return percent * (plot_top - plot_bottom) |
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def add_significance_indicator(plot, col_a=0, col_b=1, significant=False):
""" Add a p-value significance indicator. """ |
plot_bottom, plot_top = plot.get_ylim()
# Give the plot a little room for the significance indicator
line_height = vertical_percent(plot, 0.1)
# Add some extra spacing below the indicator
plot_top = plot_top + line_height
# Add some extra spacing above the indicator
plot.set_ylim(top=plot_t... |
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def stripboxplot(x, y, data, ax=None, significant=None, **kwargs):
""" Overlay a stripplot on top of a boxplot. """ |
ax = sb.boxplot(
x=x,
y=y,
data=data,
ax=ax,
fliersize=0,
**kwargs
)
plot = sb.stripplot(
x=x,
y=y,
data=data,
ax=ax,
jitter=kwargs.pop("jitter", 0.05),
color=kwargs.pop("color", "0.3"),
**kwargs
)
... |
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def fishers_exact_plot(data, condition1, condition2, ax=None, condition1_value=None, alternative="two-sided", **kwargs):
""" Perform a Fisher's exact test to com... |
plot = sb.barplot(
x=condition1,
y=condition2,
ax=ax,
data=data,
**kwargs
)
plot.set_ylabel("Percent %s" % condition2)
condition1_mask = get_condition_mask(data, condition1, condition1_value)
count_table = pd.crosstab(data[condition1], data[condition2])
... |
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def mann_whitney_plot(data, condition, distribution, ax=None, condition_value=None, alternative="two-sided", skip_plot=False, **kwargs):
""" Create a box plot co... |
condition_mask = get_condition_mask(data, condition, condition_value)
U, p_value = mannwhitneyu(
data[condition_mask][distribution],
data[~condition_mask][distribution],
alternative=alternative
)
plot = None
if not skip_plot:
plot = stripboxplot(
x=condi... |
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def roc_curve_plot(data, value_column, outcome_column, bootstrap_samples=100, ax=None):
"""Create a ROC curve and compute the bootstrap AUC for the given variabl... |
scores = bootstrap_auc(df=data,
col=value_column,
pred_col=outcome_column,
n_bootstrap=bootstrap_samples)
mean_bootstrap_auc = scores.mean()
print("{}, Bootstrap (samples = {}) AUC:{}, std={}".format(
value_column, boo... |
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def _strip_column_name(col_name, keep_paren_contents=True):
""" Utility script applying several regexs to a string. Intended to be used by `strip_column_names`. ... |
# start with input
new_col_name = col_name
# replace meaningful punctuation with text equivalents
# surround each with whitespace to enforce consistent use of _
punctuation_to_text = {
'<=': 'le',
'>=': 'ge',
'=<': 'le',
'=>': 'ge',
'<': 'lt',
'>': 'g... |
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def strip_column_names(cols, keep_paren_contents=True):
""" Utility script for renaming pandas columns to patsy-friendly names. Revised names have been: - stripp... |
# strip/replace punctuation
new_cols = [
_strip_column_name(col, keep_paren_contents=keep_paren_contents)
for col in cols]
if len(new_cols) != len(set(new_cols)):
warn_str = 'Warning: strip_column_names (if run) would introduce duplicate names.'
warn_str += ' Reverting col... |
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def set_attributes(obj, additional_data):
""" Given an object and a dictionary, give the object new attributes from that dictionary. Uses _strip_column_name to g... |
for key, value in additional_data.items():
if hasattr(obj, key):
raise ValueError("Key %s in additional_data already exists in this object" % key)
setattr(obj, _strip_column_name(key), value) |
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def return_obj(cols, df, return_cols=False):
"""Construct a DataFrameHolder and then return either that or the DataFrame.""" |
df_holder = DataFrameHolder(cols=cols, df=df)
return df_holder.return_self(return_cols=return_cols) |
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def compare_provenance( this_provenance, other_provenance, left_outer_diff = "In current but not comparison", right_outer_diff = "In comparison but not current"):... |
## if either this or other items is null, return 0
if (not this_provenance or not other_provenance):
return 0
this_items = set(this_provenance.items())
other_items = set(other_provenance.items())
# Two-way diff: are any modules introduced, and are any modules lost?
new_diff = this_ite... |
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def generate_random_missense_variants(num_variants=10, max_search=100000, reference="GRCh37"):
""" Generate a random collection of missense variants by trying ra... |
variants = []
for i in range(max_search):
bases = ["A", "C", "T", "G"]
random_ref = choice(bases)
bases.remove(random_ref)
random_alt = choice(bases)
random_contig = choice(["1", "2", "3", "4", "5"])
random_variant = Variant(contig=random_contig, start=randint(1,... |
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def generate_simple_vcf(filename, variant_collection):
""" Output a very simple metadata-free VCF for each variant in a variant_collection. """ |
contigs = []
positions = []
refs = []
alts = []
for variant in variant_collection:
contigs.append("chr" + variant.contig)
positions.append(variant.start)
refs.append(variant.ref)
alts.append(variant.alt)
df = pd.DataFrame()
df["contig"] = contigs
df["posi... |
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def list_folder(self, path):
"""Looks up folder contents of `path.`""" |
# Inspired by https://github.com/rspivak/sftpserver/blob/0.3/src/sftpserver/stub_sftp.py#L70
try:
folder_contents = []
for f in os.listdir(path):
attr = paramiko.SFTPAttributes.from_stat(os.stat(os.path.join(path, f)))
attr.filename = f
... |
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def filter_variants(variant_collection, patient, filter_fn, **kwargs):
"""Filter variants from the Variant Collection Parameters variant_collection : varcode.Var... |
if filter_fn:
return variant_collection.clone_with_new_elements([
variant
for variant in variant_collection
if filter_fn(FilterableVariant(
variant=variant,
variant_collection=variant_collection,
pat... |
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def filter_effects(effect_collection, variant_collection, patient, filter_fn, all_effects, **kwargs):
"""Filter variants from the Effect Collection Parameters ef... |
def top_priority_maybe(effect_collection):
"""
Always (unless all_effects=True) take the top priority effect per variant
so we end up with a single effect per variant.
"""
if all_effects:
return effect_collection
return EffectCollection(list(effect_collec... |
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| def count_lines_in(filename):
"Count lines in a file"
f = open(filename)
lines = 0
buf_size = 1024 * 1024
read_f = f.read # loop optimization
buf = read_f(buf_size)
while buf:
lines += buf.count('\n')
buf = read_f(buf_size)
return lines |
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| def view_name_from(path):
"Resolve a path to the full python module name of the related view function"
try:
return CACHED_VIEWS[path]
except KeyError:
view = resolve(path)
module = path
name = ''
if hasattr(view.func, '__module__'):
module = resol... |
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| def generate_table_from(data):
"Output a nicely formatted ascii table"
table = Texttable(max_width=120)
table.add_row(["view", "method", "status", "count", "minimum", "maximum", "mean", "stdev", "queries", "querytime"])
table.set_cols_align(["l", "l", "l", "r", "r", "r", "r", "r", "r", "r"])
for i... |
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| def analyze_log_file(logfile, pattern, reverse_paths=True, progress=True):
"Given a log file and regex group and extract the performance data"
if progress:
lines = count_lines_in(logfile)
pbar = ProgressBar(widgets=[Percentage(), Bar()], maxval=lines+1).start()
counter = 0
data ... |
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def to_string(self, limit=None):
""" Create a string representation of this collection, showing up to `limit` items. """ |
header = self.short_string()
if len(self) == 0:
return header
contents = ""
element_lines = [
" -- %s" % (element,)
for element in self.elements[:limit]
]
contents = "\n".join(element_lines)
if limit is not None and len(self.... |
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def safe_log_error(self, error: Exception, *info: str):
"""Log error failing silently on error""" |
self.__do_safe(lambda: self.logger.error(error, *info)) |
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def safe_log_info(self, *info: str):
"""Log info failing silently on error""" |
self.__do_safe(lambda: self.logger.info(*info)) |
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def _default_client(jws_client, reactor, key, alg):
""" Make a client if we didn't get one. """ |
if jws_client is None:
pool = HTTPConnectionPool(reactor)
agent = Agent(reactor, pool=pool)
jws_client = JWSClient(HTTPClient(agent=agent), key, alg)
return jws_client |
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def _find_supported_challenge(authzr, responders):
""" Find a challenge combination that consists of a single challenge that the responder can satisfy. :param ~a... |
matches = [
(responder, challbs[0])
for challbs in authzr.body.resolved_combinations
for responder in responders
if [challb.typ for challb in challbs] == [responder.challenge_type]]
if len(matches) == 0:
raise NoSupportedChallenges(authzr)
else:
return matche... |
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def answer_challenge(authzr, client, responders):
""" Complete an authorization using a responder. :param ~acme.messages.AuthorizationResource auth: The authoriz... |
responder, challb = _find_supported_challenge(authzr, responders)
response = challb.response(client.key)
def _stop_responding():
return maybeDeferred(
responder.stop_responding,
authzr.body.identifier.value,
challb.chall,
response)
return (
... |
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def poll_until_valid(authzr, clock, client, timeout=300.0):
""" Poll an authorization until it is in a state other than pending or processing. :param ~acme.messa... |
def repoll(result):
authzr, retry_after = result
if authzr.body.status in {STATUS_PENDING, STATUS_PROCESSING}:
return (
deferLater(clock, retry_after, lambda: None)
.addCallback(lambda _: client.poll(authzr))
.addCallback(repoll)
... |
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def from_url(cls, reactor, url, key, alg=RS256, jws_client=None):
""" Construct a client from an ACME directory at a given URL. :param url: The ``twisted.python.... |
action = LOG_ACME_CONSUME_DIRECTORY(
url=url, key_type=key.typ, alg=alg.name)
with action.context():
check_directory_url_type(url)
jws_client = _default_client(jws_client, reactor, key, alg)
return (
DeferredContext(jws_client.get(url.asTe... |
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def register(self, new_reg=None):
""" Create a new registration with the ACME server. :param ~acme.messages.NewRegistration new_reg: The registration message to ... |
if new_reg is None:
new_reg = messages.NewRegistration()
action = LOG_ACME_REGISTER(registration=new_reg)
with action.context():
return (
DeferredContext(
self.update_registration(
new_reg, uri=self.directory[ne... |
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def _maybe_registered(self, failure, new_reg):
""" If the registration already exists, we should just load it. """ |
failure.trap(ServerError)
response = failure.value.response
if response.code == http.CONFLICT:
reg = new_reg.update(
resource=messages.UpdateRegistration.resource_type)
uri = self._maybe_location(response)
return self.update_registration(reg, ... |
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def agree_to_tos(self, regr):
""" Accept the terms-of-service for a registration. :param ~acme.messages.RegistrationResource regr: The registration to update. :r... |
return self.update_registration(
regr.update(
body=regr.body.update(
agreement=regr.terms_of_service))) |
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def update_registration(self, regr, uri=None):
""" Submit a registration to the server to update it. :param ~acme.messages.RegistrationResource regr: The registr... |
if uri is None:
uri = regr.uri
if isinstance(regr, messages.RegistrationResource):
message = messages.UpdateRegistration(**dict(regr.body))
else:
message = regr
action = LOG_ACME_UPDATE_REGISTRATION(uri=uri, registration=message)
with action.c... |
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def _parse_regr_response(self, response, uri=None, new_authzr_uri=None, terms_of_service=None):
""" Parse a registration response from the server. """ |
links = _parse_header_links(response)
if u'terms-of-service' in links:
terms_of_service = links[u'terms-of-service'][u'url']
if u'next' in links:
new_authzr_uri = links[u'next'][u'url']
if new_authzr_uri is None:
raise errors.ClientError('"next" link ... |
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def _check_regr(self, regr, new_reg):
""" Check that a registration response contains the registration we were expecting. """ |
body = getattr(new_reg, 'body', new_reg)
for k, v in body.items():
if k == 'resource' or not v:
continue
if regr.body[k] != v:
raise errors.UnexpectedUpdate(regr)
if regr.body.key != self.key.public_key():
raise errors.Unexpect... |
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def request_challenges(self, identifier):
""" Create a new authorization. :param ~acme.messages.Identifier identifier: The identifier to authorize. :return: The ... |
action = LOG_ACME_CREATE_AUTHORIZATION(identifier=identifier)
with action.context():
message = messages.NewAuthorization(identifier=identifier)
return (
DeferredContext(
self._client.post(self.directory[message], message))
.add... |
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def _expect_response(cls, response, code):
""" Ensure we got the expected response code. """ |
if response.code != code:
raise errors.ClientError(
'Expected {!r} response but got {!r}'.format(
code, response.code))
return response |
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def _parse_authorization(cls, response, uri=None):
""" Parse an authorization resource. """ |
links = _parse_header_links(response)
try:
new_cert_uri = links[u'next'][u'url']
except KeyError:
raise errors.ClientError('"next" link missing')
return (
response.json()
.addCallback(
lambda body: messages.AuthorizationRes... |
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def _check_authorization(cls, authzr, identifier):
""" Check that the authorization we got is the one we expected. """ |
if authzr.body.identifier != identifier:
raise errors.UnexpectedUpdate(authzr)
return authzr |
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def answer_challenge(self, challenge_body, response):
""" Respond to an authorization challenge. :param ~acme.messages.ChallengeBody challenge_body: The challeng... |
action = LOG_ACME_ANSWER_CHALLENGE(
challenge_body=challenge_body, response=response)
with action.context():
return (
DeferredContext(
self._client.post(challenge_body.uri, response))
.addCallback(self._parse_challenge)
... |
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def _parse_challenge(cls, response):
""" Parse a challenge resource. """ |
links = _parse_header_links(response)
try:
authzr_uri = links['up']['url']
except KeyError:
raise errors.ClientError('"up" link missing')
return (
response.json()
.addCallback(
lambda body: messages.ChallengeResource(
... |
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def _check_challenge(cls, challenge, challenge_body):
""" Check that the challenge resource we got is the one we expected. """ |
if challenge.uri != challenge_body.uri:
raise errors.UnexpectedUpdate(challenge.uri)
return challenge |
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def retry_after(cls, response, default=5, _now=time.time):
""" Parse the Retry-After value from a response. """ |
val = response.headers.getRawHeaders(b'retry-after', [default])[0]
try:
return int(val)
except ValueError:
return http.stringToDatetime(val) - _now() |
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def request_issuance(self, csr):
""" Request a certificate. Authorizations should have already been completed for all of the names requested in the CSR. Note tha... |
action = LOG_ACME_REQUEST_CERTIFICATE()
with action.context():
return (
DeferredContext(
self._client.post(
self.directory[csr], csr,
content_type=DER_CONTENT_TYPE,
headers=Headers({b... |
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def _parse_certificate(cls, response):
""" Parse a response containing a certificate resource. """ |
links = _parse_header_links(response)
try:
cert_chain_uri = links[u'up'][u'url']
except KeyError:
cert_chain_uri = None
return (
response.content()
.addCallback(
lambda body: messages.CertificateResource(
... |
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def fetch_chain(self, certr, max_length=10):
""" Fetch the intermediary chain for a certificate. :param acme.messages.CertificateResource certr: The certificate ... |
action = LOG_ACME_FETCH_CHAIN()
with action.context():
if certr.cert_chain_uri is None:
return succeed([])
elif max_length < 1:
raise errors.ClientError('chain too long')
return (
DeferredContext(
se... |
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def _wrap_in_jws(self, nonce, obj):
""" Wrap ``JSONDeSerializable`` object in JWS. .. todo:: Implement ``acmePath``. :param ~josepy.interfaces.JSONDeSerializable... |
with LOG_JWS_SIGN(key_type=self._key.typ, alg=self._alg.name,
nonce=nonce):
jobj = obj.json_dumps().encode()
return (
JWS.sign(
payload=jobj, key=self._key, alg=self._alg, nonce=nonce)
.json_dumps()
... |
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def _check_response(cls, response, content_type=JSON_CONTENT_TYPE):
""" Check response content and its type. .. note:: Unlike :mod:`acme.client`, checking is str... |
def _got_failure(f):
f.trap(ValueError)
return None
def _got_json(jobj):
if 400 <= response.code < 600:
if response_ct == JSON_ERROR_CONTENT_TYPE and jobj is not None:
raise ServerError(
messages.Error.from... |
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def head(self, url, *args, **kwargs):
""" Send HEAD request without checking the response. Note that ``_check_response`` is not called, as there will be no respo... |
with LOG_JWS_HEAD().context():
return DeferredContext(
self._send_request(u'HEAD', url, *args, **kwargs)
).addActionFinish() |
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def get(self, url, content_type=JSON_CONTENT_TYPE, **kwargs):
""" Send GET request and check response. :param str method: The HTTP method to use. :param str url:... |
with LOG_JWS_GET().context():
return (
DeferredContext(self._send_request(u'GET', url, **kwargs))
.addCallback(self._check_response, content_type=content_type)
.addActionFinish()) |
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def _add_nonce(self, response):
""" Store a nonce from a response we received. :param twisted.web.iweb.IResponse response: The HTTP response. :return: The respon... |
nonce = response.headers.getRawHeaders(
REPLAY_NONCE_HEADER, [None])[0]
with LOG_JWS_ADD_NONCE(raw_nonce=nonce) as action:
if nonce is None:
raise errors.MissingNonce(response)
else:
try:
decoded_nonce = Header._fie... |
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def _get_nonce(self, url):
""" Get a nonce to use in a request, removing it from the nonces on hand. """ |
action = LOG_JWS_GET_NONCE()
if len(self._nonces) > 0:
with action:
nonce = self._nonces.pop()
action.add_success_fields(nonce=nonce)
return succeed(nonce)
else:
with action.context():
return (
... |
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def _post(self, url, obj, content_type, **kwargs):
""" POST an object and check the response. :param str url: The URL to request. :param ~josepy.interfaces.JSOND... |
with LOG_JWS_POST().context():
headers = kwargs.setdefault('headers', Headers())
headers.setRawHeaders(b'content-type', [JSON_CONTENT_TYPE])
return (
DeferredContext(self._get_nonce(url))
.addCallback(self._wrap_in_jws, obj)
.a... |
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def post(self, url, obj, content_type=JSON_CONTENT_TYPE, **kwargs):
""" POST an object and check the response. Retry once if a badNonce error is received. :param... |
def retry_bad_nonce(f):
f.trap(ServerError)
# The current RFC draft defines the namespace as
# urn:ietf:params:acme:error:<code>, but earlier drafts (and some
# current implementations) use urn:acme:error:<code> instead. We
# don't really care about t... |
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def _daemon_thread(*a, **kw):
""" Create a `threading.Thread`, but always set ``daemon``. """ |
thread = Thread(*a, **kw)
thread.daemon = True
return thread |
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def _defer_to_worker(deliver, worker, work, *args, **kwargs):
""" Run a task in a worker, delivering the result as a ``Deferred`` in the reactor thread. """ |
deferred = Deferred()
def wrapped_work():
try:
result = work(*args, **kwargs)
except BaseException:
f = Failure()
deliver(lambda: deferred.errback(f))
else:
deliver(lambda: deferred.callback(result))
worker.do(wrapped_work)
return... |
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def _split_zone(server_name, zone_name):
""" Split the zone portion off from a DNS label. :param str server_name: The full DNS label. :param str zone_name: The z... |
server_name = server_name.rstrip(u'.')
zone_name = zone_name.rstrip(u'.')
if not (server_name == zone_name or
server_name.endswith(u'.' + zone_name)):
raise NotInZone(server_name=server_name, zone_name=zone_name)
return server_name[:-len(zone_name)].rstrip(u'.') |
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def _get_existing(driver, zone_name, server_name, validation):
""" Get existing validation records. """ |
if zone_name is None:
zones = sorted(
(z for z
in driver.list_zones()
if server_name.rstrip(u'.')
.endswith(u'.' + z.domain.rstrip(u'.'))),
key=lambda z: len(z.domain),
reverse=True)
if len(zones) == 0:
raise ... |
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def _validation(response):
""" Get the validation value for a challenge response. """ |
h = hashlib.sha256(response.key_authorization.encode("utf-8"))
return b64encode(h.digest()).decode() |
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def load_or_create_client_key(pem_path):
""" Load the client key from a directory, creating it if it does not exist. .. note:: The client key that will be create... |
acme_key_file = pem_path.asTextMode().child(u'client.key')
if acme_key_file.exists():
key = serialization.load_pem_private_key(
acme_key_file.getContent(),
password=None,
backend=default_backend())
else:
key = generate_private_key(u'rsa')
acme_key... |
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def _parse(reactor, directory, pemdir, *args, **kwargs):
""" Parse a txacme endpoint description. :param reactor: The Twisted reactor. :param directory: ``twiste... |
def colon_join(items):
return ':'.join([item.replace(':', '\\:') for item in items])
sub = colon_join(list(args) + ['='.join(item) for item in kwargs.items()])
pem_path = FilePath(pemdir).asTextMode()
acme_key = load_or_create_client_key(pem_path)
return AutoTLSEndpoint(
reactor=rea... |
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def lazyread(f, delimiter):
""" Generator which continually reads ``f`` to the next instance of ``delimiter``. This allows you to do batch processing on the cont... |
# Get an empty string to start with. We need to make sure that if the
# file is opened in binary mode, we're using byte strings, and similar
# for Unicode. Otherwise trying to update the running string will
# hit a TypeError.
try:
running = f.read(0)
except Exception as e:
# ... |
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def generate_private_key(key_type):
""" Generate a random private key using sensible parameters. :param str key_type: The type of key to generate. One of: ``rsa`... |
if key_type == u'rsa':
return rsa.generate_private_key(
public_exponent=65537, key_size=2048, backend=default_backend())
raise ValueError(key_type) |
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def tap(f):
""" "Tap" a Deferred callback chain with a function whose return value is ignored. """ |
@wraps(f)
def _cb(res, *a, **kw):
d = maybeDeferred(f, res, *a, **kw)
d.addCallback(lambda ignored: res)
return d
return _cb |
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def decode_csr(b64der):
""" Decode JOSE Base-64 DER-encoded CSR. :param str b64der: The encoded CSR. :rtype: `cryptography.x509.CertificateSigningRequest` :retur... |
try:
return x509.load_der_x509_csr(
decode_b64jose(b64der), default_backend())
except ValueError as error:
raise DeserializationError(error) |
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def csr_for_names(names, key):
""" Generate a certificate signing request for the given names and private key. .. seealso:: `acme.client.Client.request_issuance`... |
if len(names) == 0:
raise ValueError('Must have at least one name')
if len(names[0]) > 64:
common_name = u'san.too.long.invalid'
else:
common_name = names[0]
return (
x509.CertificateSigningRequestBuilder()
.subject_name(x509.Name([
x509.NameAttribute... |
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def _wrap_parse(code, filename):
""" async wrapper is required to avoid await calls raising a SyntaxError """ |
code = 'async def wrapper():\n' + indent(code, ' ')
return ast.parse(code, filename=filename).body[0].body[0].value |
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def layers_to_solr(self, layers):
""" Sync n layers in Solr. """ |
layers_dict_list = []
layers_success_ids = []
layers_errors_ids = []
for layer in layers:
layer_dict, message = layer2dict(layer)
if not layer_dict:
layers_errors_ids.append([layer.id, message])
LOGGER.error(message)
... |
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def layer_to_solr(self, layer):
""" Sync a layer in Solr. """ |
success = True
message = 'Synced layer id %s to Solr' % layer.id
layer_dict, message = layer2dict(layer)
if not layer_dict:
success = False
else:
layer_json = json.dumps(layer_dict)
try:
url_solr_update = '%s/solr/hypermap/upd... |
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def clear_solr(self, catalog="hypermap"):
"""Clear all indexes in the solr core""" |
solr_url = "{0}/solr/{1}".format(SEARCH_URL, catalog)
solr = pysolr.Solr(solr_url, timeout=60)
solr.delete(q='*:*')
LOGGER.debug('Solr core cleared') |
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def create_service_from_endpoint(endpoint, service_type, title=None, abstract=None, catalog=None):
""" Create a service from an endpoint if it does not already e... |
from models import Service
if Service.objects.filter(url=endpoint, catalog=catalog).count() == 0:
# check if endpoint is valid
request = requests.get(endpoint)
if request.status_code == 200:
LOGGER.debug('Creating a %s service for endpoint=%s catalog=%s' % (service_type, end... |
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def service_url_parse(url):
""" Function that parses from url the service and folder of services. """ |
endpoint = get_sanitized_endpoint(url)
url_split_list = url.split(endpoint + '/')
if len(url_split_list) != 0:
url_split_list = url_split_list[1].split('/')
else:
raise Exception('Wrong url parsed')
# Remove unnecessary items from list of the split url.
parsed_url = [s for s in... |
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def inverse_mercator(xy):
""" Given coordinates in spherical mercator, return a lon,lat tuple. """ |
lon = (xy[0] / 20037508.34) * 180
lat = (xy[1] / 20037508.34) * 180
lat = 180 / math.pi * \
(2 * math.atan(math.exp(lat * math.pi / 180)) - math.pi / 2)
return (lon, lat) |
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def get_wms_version_negotiate(url, timeout=10):
""" OWSLib wrapper function to perform version negotiation against owslib.wms.WebMapService """ |
try:
LOGGER.debug('Trying a WMS 1.3.0 GetCapabilities request')
return WebMapService(url, version='1.3.0', timeout=timeout)
except Exception as err:
LOGGER.warning('WMS 1.3.0 support not found: %s', err)
LOGGER.debug('Trying a WMS 1.1.1 GetCapabilities request instead')
... |
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def get_sanitized_endpoint(url):
""" Sanitize an endpoint, as removing unneeded parameters """ |
# sanitize esri
sanitized_url = url.rstrip()
esri_string = '/rest/services'
if esri_string in url:
match = re.search(esri_string, sanitized_url)
sanitized_url = url[0:(match.start(0)+len(esri_string))]
return sanitized_url |
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def get_esri_extent(esriobj):
""" Get the extent of an ESRI resource """ |
extent = None
srs = None
if 'fullExtent' in esriobj._json_struct:
extent = esriobj._json_struct['fullExtent']
if 'extent' in esriobj._json_struct:
extent = esriobj._json_struct['extent']
try:
srs = extent['spatialReference']['wkid']
except KeyError, err:
LOGGE... |
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def bbox2wktpolygon(bbox):
""" Return OGC WKT Polygon of a simple bbox list of strings """ |
minx = float(bbox[0])
miny = float(bbox[1])
maxx = float(bbox[2])
maxy = float(bbox[3])
return 'POLYGON((%.2f %.2f, %.2f %.2f, %.2f %.2f, %.2f %.2f, %.2f %.2f))' \
% (minx, miny, minx, maxy, maxx, maxy, maxx, miny, minx, miny) |
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def get_solr_date(pydate, is_negative):
""" Returns a date in a valid Solr format from a string. """ |
# check if date is valid and then set it to solr format YYYY-MM-DDThh:mm:ssZ
try:
if isinstance(pydate, datetime.datetime):
solr_date = '%sZ' % pydate.isoformat()[0:19]
if is_negative:
LOGGER.debug('%s This layer has a negative date' % solr_date)
... |
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def get_date(layer):
""" Returns a custom date representation. A date can be detected or from metadata. It can be a range or a simple date in isoformat. """ |
date = None
sign = '+'
date_type = 1
layer_dates = layer.get_layer_dates()
# we index the first date!
if layer_dates:
sign = layer_dates[0][0]
date = layer_dates[0][1]
date_type = layer_dates[0][2]
if date is None:
date = layer.created
# layer date > 2300... |
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def detect_metadata_url_scheme(url):
"""detect whether a url is a Service type that HHypermap supports""" |
scheme = None
url_lower = url.lower()
if any(x in url_lower for x in ['wms', 'service=wms']):
scheme = 'OGC:WMS'
if any(x in url_lower for x in ['wmts', 'service=wmts']):
scheme = 'OGC:WMTS'
elif all(x in url for x in ['/MapServer', 'f=json']):
scheme = 'ESRI:ArcGIS:MapSer... |
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def serialize_checks(check_set):
""" Serialize a check_set for raphael """ |
check_set_list = []
for check in check_set.all()[:25]:
check_set_list.append(
{
'datetime': check.checked_datetime.isoformat(),
'value': check.response_time,
'success': 1 if check.success else 0
}
)
return check_set_lis... |
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def domains(request):
""" A page with number of services and layers faceted on domains. """ |
url = ''
query = '*:*&facet=true&facet.limit=-1&facet.pivot=domain_name,service_id&wt=json&indent=true&rows=0'
if settings.SEARCH_TYPE == 'elasticsearch':
url = '%s/select?q=%s' % (settings.SEARCH_URL, query)
if settings.SEARCH_TYPE == 'solr':
url = '%s/solr/hypermap/select?q=%s' % (set... |
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def tasks_runner(request):
""" A page that let the admin to run global tasks. """ |
# server info
cached_layers_number = 0
cached_layers = cache.get('layers')
if cached_layers:
cached_layers_number = len(cached_layers)
cached_deleted_layers_number = 0
cached_deleted_layers = cache.get('deleted_layers')
if cached_deleted_layers:
cached_deleted_layers_numbe... |
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def layer_mapproxy(request, catalog_slug, layer_uuid, path_info):
""" Get Layer with matching catalog and uuid """ |
layer = get_object_or_404(Layer,
uuid=layer_uuid,
catalog__slug=catalog_slug)
# for WorldMap layers we need to use the url of the layer
if layer.service.type == 'Hypermap:WorldMap':
layer.service.url = layer.url
# Set up a mapproxy a... |
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def parse_datetime(date_str):
""" Parses a date string to date object. for BCE dates, only supports the year part. """ |
is_common_era = True
date_str_parts = date_str.split("-")
if date_str_parts and date_str_parts[0] == '':
is_common_era = False
# for now, only support BCE years
# assume the datetime comes complete, but
# when it comes only the year, add the missing datetime info:
i... |
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def query_ids(self, ids):
""" Query by list of identifiers """ |
results = self._get_repo_filter(Layer.objects).filter(uuid__in=ids).all()
if len(results) == 0: # try services
results = self._get_repo_filter(Service.objects).filter(uuid__in=ids).all()
return results |
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def query_domain(self, domain, typenames, domainquerytype='list', count=False):
""" Query by property domain values """ |
objects = self._get_repo_filter(Layer.objects)
if domainquerytype == 'range':
return [tuple(objects.aggregate(Min(domain), Max(domain)).values())]
else:
if count:
return [(d[domain], d['%s__count' % domain])
for d in objects.valu... |
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def query_source(self, source):
""" Query by source """ |
return self._get_repo_filter(Layer.objects).filter(url=source) |
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def query(self, constraint, sortby=None, typenames=None, maxrecords=10, startposition=0):
""" Query records from underlying repository """ |
# run the raw query and get total
# we want to exclude layers which are not valid, as it is done in the search engine
if 'where' in constraint: # GetRecords with constraint
query = self._get_repo_filter(Layer.objects).filter(
is_valid=True).extra(where=[constraint[... |
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def insert(self, resourcetype, source, insert_date=None):
""" Insert a record into the repository """ |
caller = inspect.stack()[1][3]
if caller == 'transaction': # insert of Layer
hhclass = 'Layer'
source = resourcetype
resourcetype = resourcetype.csw_schema
else: # insert of service
hhclass = 'Service'
if resourcetype not in HYPERM... |
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