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genialis/resolwe | resolwe/elastic/builder.py | Dependency.connect | def connect(self, index):
"""Connect signals needed for dependency updates.
Pre- and post-delete signals have to be handled separately, as:
* in the pre-delete signal we have the information which
objects to rebuild, but affected relations are still
presented, so rebu... | python | def connect(self, index):
"""Connect signals needed for dependency updates.
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.connect | def connect(self, index):
"""Connect signals needed for dependency updates."""
# Determine which model is the target model as either side of the relation
# may be passed as `field`.
if index.object_type == self.field.rel.model:
self.model = self.field.rel.related_model
... | python | def connect(self, index):
"""Connect signals needed for dependency updates."""
# Determine which model is the target model as either side of the relation
# may be passed as `field`.
if index.object_type == self.field.rel.model:
self.model = self.field.rel.related_model
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency._filter | def _filter(self, objects, **kwargs):
"""Determine if dependent object should be processed."""
for obj in objects:
if self.filter(obj, **kwargs) is False:
return False
return True | python | def _filter(self, objects, **kwargs):
"""Determine if dependent object should be processed."""
for obj in objects:
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return False
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency._get_build_kwargs | def _get_build_kwargs(self, obj, pk_set=None, action=None, update_fields=None, reverse=None, **kwargs):
"""Prepare arguments for rebuilding indices."""
if action is None:
# Check filter before rebuilding index.
if not self._filter([obj], update_fields=update_fields):
... | python | def _get_build_kwargs(self, obj, pk_set=None, action=None, update_fields=None, reverse=None, **kwargs):
"""Prepare arguments for rebuilding indices."""
if action is None:
# Check filter before rebuilding index.
if not self._filter([obj], update_fields=update_fields):
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process_predelete | def process_predelete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Render the queryset of influenced objects and cache it."""
build_kwargs = self._get_build_kwargs(obj, pk_set, action, update_fields, **kwargs)
self.delete_cache.set(obj, build_kwargs) | python | def process_predelete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Render the queryset of influenced objects and cache it."""
build_kwargs = self._get_build_kwargs(obj, pk_set, action, update_fields, **kwargs)
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process_delete | def process_delete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Recreate queryset from the index and rebuild the index."""
build_kwargs = self.delete_cache.take(obj)
if build_kwargs:
self.index.build(**build_kwargs) | python | def process_delete(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Recreate queryset from the index and rebuild the index."""
build_kwargs = self.delete_cache.take(obj)
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process_m2m | def process_m2m(self, obj, pk_set=None, action=None, update_fields=None, cache_key=None, **kwargs):
"""Process signals from dependencies.
Remove signal is processed in two parts. For details see:
:func:`~Dependency.connect`
"""
if action not in (None, 'post_add', 'pre_remove', '... | python | def process_m2m(self, obj, pk_set=None, action=None, update_fields=None, cache_key=None, **kwargs):
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency._process_m2m_through | def _process_m2m_through(self, obj, action):
"""Process custom M2M through model actions."""
source = getattr(obj, self.field.rel.field.m2m_field_name())
target = getattr(obj, self.field.rel.field.m2m_reverse_field_name())
pk_set = set()
if target:
pk_set.add(target.... | python | def _process_m2m_through(self, obj, action):
"""Process custom M2M through model actions."""
source = getattr(obj, self.field.rel.field.m2m_field_name())
target = getattr(obj, self.field.rel.field.m2m_reverse_field_name())
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process_m2m_through_save | def process_m2m_through_save(self, obj, created=False, **kwargs):
"""Process M2M post save for custom through model."""
# We are only interested in signals that establish relations.
if not created:
return
self._process_m2m_through(obj, 'post_add') | python | def process_m2m_through_save(self, obj, created=False, **kwargs):
"""Process M2M post save for custom through model."""
# We are only interested in signals that establish relations.
if not created:
return
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genialis/resolwe | resolwe/elastic/builder.py | ManyToManyDependency.process | def process(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
"""Process signals from dependencies."""
build_kwargs = self._get_build_kwargs(obj, pk_set, action, update_fields, **kwargs)
if build_kwargs:
self.index.build(**build_kwargs) | python | def process(self, obj, pk_set=None, action=None, update_fields=None, **kwargs):
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build_kwargs = self._get_build_kwargs(obj, pk_set, action, update_fields, **kwargs)
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder._connect_signal | def _connect_signal(self, index):
"""Create signals for building indexes."""
post_save_signal = ElasticSignal(index, 'build')
post_save_signal.connect(post_save, sender=index.object_type)
self.signals.append(post_save_signal)
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post_save_signal = ElasticSignal(index, 'build')
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.register_signals | def register_signals(self):
"""Register signals for all indexes."""
for index in self.indexes:
if index.object_type:
self._connect_signal(index) | python | def register_signals(self):
"""Register signals for all indexes."""
for index in self.indexes:
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.discover_indexes | def discover_indexes(self):
"""Save list of index builders into ``_index_builders``."""
self.indexes = []
for app_config in apps.get_app_configs():
indexes_path = '{}.elastic_indexes'.format(app_config.name)
try:
indexes_module = import_module(indexes_pat... | python | def discover_indexes(self):
"""Save list of index builders into ``_index_builders``."""
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indexes_path = '{}.elastic_indexes'.format(app_config.name)
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.build | def build(self, obj=None, queryset=None, push=True):
"""Trigger building of the indexes.
Support passing ``obj`` parameter to the indexes, so we can
trigger build only for one object.
"""
for index in self.indexes:
index.build(obj, queryset, push) | python | def build(self, obj=None, queryset=None, push=True):
"""Trigger building of the indexes.
Support passing ``obj`` parameter to the indexes, so we can
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.push | def push(self, index=None):
"""Push built documents to ElasticSearch.
If ``index`` is specified, only that index will be pushed.
"""
for ind in self.indexes:
if index and not isinstance(ind, index):
continue
ind.push() | python | def push(self, index=None):
"""Push built documents to ElasticSearch.
If ``index`` is specified, only that index will be pushed.
"""
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if index and not isinstance(ind, index):
continue
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.delete | def delete(self, skip_mapping=False):
"""Delete all entries from ElasticSearch."""
for index in self.indexes:
index.destroy()
if not skip_mapping:
index.create_mapping() | python | def delete(self, skip_mapping=False):
"""Delete all entries from ElasticSearch."""
for index in self.indexes:
index.destroy()
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genialis/resolwe | resolwe/elastic/builder.py | IndexBuilder.destroy | def destroy(self):
"""Delete all indexes from Elasticsearch and index builder."""
self.unregister_signals()
for index in self.indexes:
index.destroy()
self.indexes = [] | python | def destroy(self):
"""Delete all indexes from Elasticsearch and index builder."""
self.unregister_signals()
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._set_initial | def _set_initial(self, C_in, scale_in):
r"""Set the initial values for parameters and Wilson coefficients at
the scale `scale_in`."""
self.C_in = C_in
self.scale_in = scale_in | python | def _set_initial(self, C_in, scale_in):
r"""Set the initial values for parameters and Wilson coefficients at
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self.C_in = C_in
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._set_initial_wcxf | def _set_initial_wcxf(self, wc, get_smpar=True):
"""Load the initial values for Wilson coefficients from a
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... | python | def _set_initial_wcxf(self, wc, get_smpar=True):
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._to_wcxf | def _to_wcxf(self, C_out, scale_out):
"""Return the Wilson coefficients `C_out` as a wcxf.WC instance.
Note that the Wilson coefficients are rotated into the Warsaw basis
as defined in WCxf, i.e. to the basis where the down-type and charged
lepton mass matrices are diagonal."""
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"""Return the Wilson coefficients `C_out` as a wcxf.WC instance.
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._rgevolve | def _rgevolve(self, scale_out, **kwargs):
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Returns a dictionary with parameters and Wilson coefficients at
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._rgevolve_leadinglog | def _rgevolve_leadinglog(self, scale_out):
"""Compute the leading logarithmic approximation to the solution
of the SMEFT RGEs from the initial scale to `scale_out`.
Returns a dictionary with parameters and Wilson coefficients.
Much faster but less precise that `rgevolve`.
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._run_sm_scale_in | def _run_sm_scale_in(self, C_out, scale_sm=91.1876):
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input scale."""
# initialize an empty SMEFT instance
smeft_sm = SMEFT(wc=None)
C_in_sm = ... | python | def _run_sm_scale_in(self, C_out, scale_sm=91.1876):
"""Get the SM parameters at the EW scale, using an estimate `C_out`
of the Wilson coefficients at that scale, and run them to the
input scale."""
# initialize an empty SMEFT instance
smeft_sm = SMEFT(wc=None)
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT.get_smpar | def get_smpar(self, accuracy='integrate', scale_sm=91.1876):
"""Compute the SM MS-bar parameters at the electroweak scale.
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT._get_sm_scale_in | def _get_sm_scale_in(self, scale_sm=91.1876):
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scale).
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT.run | def run(self, scale, accuracy='integrate', **kwargs):
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wilson-eft/wilson | wilson/run/smeft/classes.py | SMEFT.run_continuous | def run_continuous(self, scale):
"""Return a continuous solution to the RGE as `RGsolution` instance."""
if scale == self.scale_in:
raise ValueError("The scale must be different from the input scale")
elif scale < self.scale_in:
scale_min = scale
scale_max = s... | python | def run_continuous(self, scale):
"""Return a continuous solution to the RGE as `RGsolution` instance."""
if scale == self.scale_in:
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genialis/resolwe | resolwe/flow/models/fields.py | ResolweSlugField.deconstruct | def deconstruct(self):
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name, path, args, kwargs = super().deconstruct()
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kwargs['unique_with'] = self.unique_with
kwar... | python | def deconstruct(self):
"""Deconstruct method."""
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genialis/resolwe | resolwe/flow/models/fields.py | ResolweSlugField._get_populate_from_value | def _get_populate_from_value(self, instance):
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genialis/resolwe | resolwe/flow/models/fields.py | ResolweSlugField.pre_save | def pre_save(self, instance, add):
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genialis/resolwe | resolwe/flow/execution_engines/workflow/__init__.py | ExecutionEngine.discover_process | def discover_process(self, path):
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"""
if not path.lower().endswith(('.yml', '.yaml')):
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genialis/resolwe | resolwe/flow/execution_engines/workflow/__init__.py | ExecutionEngine._evaluate_expressions | def _evaluate_expressions(self, expression_engine, step_id, values, context):
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genialis/resolwe | resolwe/flow/execution_engines/workflow/__init__.py | ExecutionEngine.evaluate | def evaluate(self, data):
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... | python | async def init():
"""Create a connection to the Redis server."""
global redis_conn # pylint: disable=global-statement,invalid-name
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:param expect_reply: If ``True``, wait for the manager to reply
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:param extra_fields: A di... | python | async def send_manager_command(cmd, expect_reply=True, extra_fields={}):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | extract_values_query | def extract_values_query(query, field_list, out_stream=None):
"""Get list of dicts where each dict holds values from one SciObj.
Args:
field_list: list of str
List of field names for which to return values. Must be strings from
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | extract_values | def extract_values(field_list=None, filter_arg_dict=None, out_stream=None):
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Args:
field_list: list of str
List of field names for which to return values. Must be strings from
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | assert_invalid_field_list | def assert_invalid_field_list(field_list):
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"""
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invalid... | python | def assert_invalid_field_list(field_list):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | _annotate_query | def _annotate_query(query, generate_dict):
"""Add annotations to the query to retrieve values required by field value generate
functions."""
annotate_key_list = []
for field_name, annotate_dict in generate_dict.items():
for annotate_name, annotate_func in annotate_dict["annotate_dict"].items():
... | python | def _annotate_query(query, generate_dict):
"""Add annotations to the query to retrieve values required by field value generate
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | _value_list_to_sciobj_dict | def _value_list_to_sciobj_dict(
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sciobj_dict = {}
# for sciobj_value, lookup_str in zip(sciobj_value_list, lookup_list):
lookup_to_... | python | def _value_list_to_sciobj_dict(
sciobj_value_list, lookup_list, lookup_dict, generate_dict
):
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sciobj_dict = {}
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta_extract.py | _split_field_list | def _split_field_list(field_list):
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methods.
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/util.py | dataoneTypes | def dataoneTypes(request):
"""Return the PyXB binding to use when handling a request."""
if is_v1_api(request):
return d1_common.types.dataoneTypes_v1_1
elif is_v2_api(request) or is_diag_api(request):
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else:
raise d1_common.types.exception... | python | def dataoneTypes(request):
"""Return the PyXB binding to use when handling a request."""
if is_v1_api(request):
return d1_common.types.dataoneTypes_v1_1
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DataONEorg/d1_python | gmn/src/d1_gmn/app/views/util.py | parse_and_normalize_url_date | def parse_and_normalize_url_date(date_str):
"""Parse a ISO 8601 date-time with optional timezone.
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- Return naive date-time set to UTC.
"""
if date_str is None:
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.get | def get(self, doc_id):
"""Retrieve the specified document."""
resp_dict = self._get_query(q='id:{}'.format(doc_id))
if resp_dict['response']['numFound'] > 0:
return resp_dict['response']['docs'][0] | python | def get(self, doc_id):
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.get_ids | def get_ids(self, start=0, rows=1000, **query_dict):
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.count | def count(self, **query_dict):
"""Return the number of entries that match query."""
param_dict = query_dict.copy()
param_dict['count'] = 0
resp_dict = self._get_query(**param_dict)
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param_dict = query_dict.copy()
param_dict['count'] = 0
resp_dict = self._get_query(**param_dict)
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.get_field_values | def get_field_values(self, name, maxvalues=-1, sort=True, **query_dict):
"""Retrieve the unique values for a field, along with their usage counts.
:param name: Name of field for which to retrieve values
:type name: string
:param sort: Sort the result
:param maxvalues: Maximum ... | python | def get_field_values(self, name, maxvalues=-1, sort=True, **query_dict):
"""Retrieve the unique values for a field, along with their usage counts.
:param name: Name of field for which to retrieve values
:type name: string
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.get_field_min_max | def get_field_min_max(self, name, **query_dict):
"""Returns the minimum and maximum values of the specified field. This requires
two search calls to the service, each requesting a single value of a single
field.
@param name(string) Name of the field
@param q(string) Query identi... | python | def get_field_min_max(self, name, **query_dict):
"""Returns the minimum and maximum values of the specified field. This requires
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.field_alpha_histogram | def field_alpha_histogram(
self, name, n_bins=10, include_queries=True, **query_dict
):
"""Generates a histogram of values from a string field.
Output is: [[low, high, count, query], ... ]. Bin edges is determined by equal
division of the fields.
"""
bin_list = []
... | python | def field_alpha_histogram(
self, name, n_bins=10, include_queries=True, **query_dict
):
"""Generates a histogram of values from a string field.
Output is: [[low, high, count, query], ... ]. Bin edges is determined by equal
division of the fields.
"""
bin_list = []
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient.add_docs | def add_docs(self, docs):
"""docs is a list of fields that are a dictionary of name:value for a record."""
return self.query(
'solr',
'<add>{}</add>'.format(
''.join([self._format_add(fields) for fields in docs])
),
do_post=True,
) | python | def add_docs(self, docs):
"""docs is a list of fields that are a dictionary of name:value for a record."""
return self.query(
'solr',
'<add>{}</add>'.format(
''.join([self._format_add(fields) for fields in docs])
),
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._coerce_type | def _coerce_type(self, field_type, value):
"""Returns unicode(value) after trying to coerce it into the Solr field type.
@param field_type(string) The Solr field type for the value
@param value(any) The value that is to be represented as Unicode text.
"""
if value is None:
... | python | def _coerce_type(self, field_type, value):
"""Returns unicode(value) after trying to coerce it into the Solr field type.
@param field_type(string) The Solr field type for the value
@param value(any) The value that is to be represented as Unicode text.
"""
if value is None:
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._get_solr_type | def _get_solr_type(self, field):
"""Returns the Solr type of the specified field name.
Assumes the convention of dynamic fields using an underscore + type character
code for the field name.
"""
field_type = 'string'
try:
field_type = FIELD_TYPE_CONVERSION_MA... | python | def _get_solr_type(self, field):
"""Returns the Solr type of the specified field name.
Assumes the convention of dynamic fields using an underscore + type character
code for the field name.
"""
field_type = 'string'
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field_type = FIELD_TYPE_CONVERSION_MA... | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._get_query | def _get_query(self, **query_dict):
"""Perform a GET query against Solr and return the response as a Python dict."""
param_dict = query_dict.copy()
return self._send_query(do_post=False, **param_dict) | python | def _get_query(self, **query_dict):
"""Perform a GET query against Solr and return the response as a Python dict."""
param_dict = query_dict.copy()
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._post_query | def _post_query(self, **query_dict):
"""Perform a POST query against Solr and return the response as a Python
dict."""
param_dict = query_dict.copy()
return self._send_query(do_post=True, **param_dict) | python | def _post_query(self, **query_dict):
"""Perform a POST query against Solr and return the response as a Python
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param_dict = query_dict.copy()
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._send_query | def _send_query(self, do_post=False, **query_dict):
"""Perform a query against Solr and return the response as a Python dict."""
# self._prepare_query_term()
param_dict = query_dict.copy()
param_dict.setdefault('wt', 'json')
param_dict.setdefault('q', '*.*')
param_dict.se... | python | def _send_query(self, do_post=False, **query_dict):
"""Perform a query against Solr and return the response as a Python dict."""
# self._prepare_query_term()
param_dict = query_dict.copy()
param_dict.setdefault('wt', 'json')
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._prepare_query_term | def _prepare_query_term(self, field, term):
"""Prepare a query term for inclusion in a query.
This escapes the term and if necessary, wraps the term in quotes.
"""
if term == "*":
return term
add_star = False
if term[len(term) - 1] == '*':
add_st... | python | def _prepare_query_term(self, field, term):
"""Prepare a query term for inclusion in a query.
This escapes the term and if necessary, wraps the term in quotes.
"""
if term == "*":
return term
add_star = False
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrClient._escape_query_term | def _escape_query_term(self, term):
"""Escape a query term for inclusion in a query.
- Also see: prepare_query_term().
"""
term = term.replace('\\', '\\\\')
for c in RESERVED_CHAR_LIST:
term = term.replace(c, r'\{}'.format(c))
return term | python | def _escape_query_term(self, term):
"""Escape a query term for inclusion in a query.
- Also see: prepare_query_term().
"""
term = term.replace('\\', '\\\\')
for c in RESERVED_CHAR_LIST:
term = term.replace(c, r'\{}'.format(c))
return term | [
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrSearchResponseIterator._next_page | def _next_page(self, offset):
"""Retrieves the next set of results from the service."""
self._log.debug("Iterator c_record={}".format(self.c_record))
page_size = self.page_size
if (offset + page_size) > self.max_records:
page_size = self.max_records - offset
param_dic... | python | def _next_page(self, offset):
"""Retrieves the next set of results from the service."""
self._log.debug("Iterator c_record={}".format(self.c_record))
page_size = self.page_size
if (offset + page_size) > self.max_records:
page_size = self.max_records - offset
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DataONEorg/d1_python | lib_client/src/d1_client/solr_client.py | SolrValuesResponseIterator._next_page | def _next_page(self, offset):
"""Retrieves the next set of results from the service."""
self._log.debug("Iterator c_record={}".format(self.c_record))
param_dict = self.query_dict.copy()
param_dict.update(
{
'rows': '0',
'facet': 'true',
... | python | def _next_page(self, offset):
"""Retrieves the next set of results from the service."""
self._log.debug("Iterator c_record={}".format(self.c_record))
param_dict = self.query_dict.copy()
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genialis/resolwe | resolwe/flow/migrations/0023_process_entity_2.py | migrate_flow_collection | def migrate_flow_collection(apps, schema_editor):
"""Migrate 'flow_collection' field to 'entity_type'."""
Process = apps.get_model('flow', 'Process')
DescriptorSchema = apps.get_model('flow', 'DescriptorSchema')
for process in Process.objects.all():
process.entity_type = process.flow_collection... | python | def migrate_flow_collection(apps, schema_editor):
"""Migrate 'flow_collection' field to 'entity_type'."""
Process = apps.get_model('flow', 'Process')
DescriptorSchema = apps.get_model('flow', 'DescriptorSchema')
for process in Process.objects.all():
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | get_pyxb_binding_by_api_version | def get_pyxb_binding_by_api_version(api_major, api_minor=0):
"""Map DataONE API version tag to PyXB binding.
Given a DataONE API major version number, return PyXB binding that can
serialize and deserialize DataONE XML docs of that version.
Args:
api_major, api_minor: str or int
DataONE A... | python | def get_pyxb_binding_by_api_version(api_major, api_minor=0):
"""Map DataONE API version tag to PyXB binding.
Given a DataONE API major version number, return PyXB binding that can
serialize and deserialize DataONE XML docs of that version.
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api_major, api_minor: str or int
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | extract_version_tag_from_url | def extract_version_tag_from_url(url):
"""Extract a DataONE API version tag from a MN or CN service endpoint URL.
Args:
url : str
Service endpoint URL. E.g.: ``https://mn.example.org/path/v2/object/pid``.
Returns:
str : Valid version tags are currently ``v1`` or ``v2``.
"""
m ... | python | def extract_version_tag_from_url(url):
"""Extract a DataONE API version tag from a MN or CN service endpoint URL.
Args:
url : str
Service endpoint URL. E.g.: ``https://mn.example.org/path/v2/object/pid``.
Returns:
str : Valid version tags are currently ``v1`` or ``v2``.
"""
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | str_to_v1_str | def str_to_v1_str(xml_str):
"""Convert a API v2 XML doc to v1 XML doc.
Removes elements that are only valid for v2 and changes namespace to v1.
If doc is already v1, it is returned unchanged.
Args:
xml_str : str
API v2 XML doc. E.g.: ``SystemMetadata v2``.
Returns:
str : API ... | python | def str_to_v1_str(xml_str):
"""Convert a API v2 XML doc to v1 XML doc.
Removes elements that are only valid for v2 and changes namespace to v1.
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xml_str : str
API v2 XML doc. E.g.: ``SystemMetadata v2``.
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | str_to_v2_str | def str_to_v2_str(xml_str):
"""Convert a API v1 XML doc to v2 XML doc.
All v1 elements are valid for v2, so only changes namespace.
Args:
xml_str : str
API v1 XML doc. E.g.: ``SystemMetadata v1``.
Returns:
str : API v2 XML doc. E.g.: ``SystemMetadata v2``.
"""
if str_is_v... | python | def str_to_v2_str(xml_str):
"""Convert a API v1 XML doc to v2 XML doc.
All v1 elements are valid for v2, so only changes namespace.
Args:
xml_str : str
API v1 XML doc. E.g.: ``SystemMetadata v1``.
Returns:
str : API v2 XML doc. E.g.: ``SystemMetadata v2``.
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | str_is_well_formed | def str_is_well_formed(xml_str):
"""
Args:
xml_str : str
DataONE API XML doc.
Returns:
bool: **True** if XML doc is well formed.
"""
try:
str_to_etree(xml_str)
except xml.etree.ElementTree.ParseError:
return False
else:
return True | python | def str_is_well_formed(xml_str):
"""
Args:
xml_str : str
DataONE API XML doc.
Returns:
bool: **True** if XML doc is well formed.
"""
try:
str_to_etree(xml_str)
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | pyxb_is_v1 | def pyxb_is_v1(pyxb_obj):
"""
Args:
pyxb_obj : PyXB object
PyXB object holding an unknown type.
Returns:
bool: **True** if ``pyxb_obj`` holds an API v1 type.
"""
# TODO: Will not detect v1.2 as v1.
return (
pyxb_obj._element().name().namespace()
== d1_common.types.dataon... | python | def pyxb_is_v1(pyxb_obj):
"""
Args:
pyxb_obj : PyXB object
PyXB object holding an unknown type.
Returns:
bool: **True** if ``pyxb_obj`` holds an API v1 type.
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | pyxb_is_v2 | def pyxb_is_v2(pyxb_obj):
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Args:
pyxb_obj : PyXB object
PyXB object holding an unknown type.
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pyxb_obj : PyXB object
PyXB object holding an unknown type.
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | str_to_etree | def str_to_etree(xml_str, encoding='utf-8'):
"""Deserialize API XML doc to an ElementTree.
Args:
xml_str: bytes
DataONE API XML doc
encoding: str
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Returns:
ElementTree: Matching the API version of the ... | python | def str_to_etree(xml_str, encoding='utf-8'):
"""Deserialize API XML doc to an ElementTree.
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xml_str: bytes
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | replace_namespace_with_prefix | def replace_namespace_with_prefix(tag_str, ns_reverse_dict=None):
"""Convert XML tag names with namespace on the form ``{namespace}tag`` to form
``prefix:tag``.
Args:
tag_str: str
Tag name with namespace. E.g.:
``{http://www.openarchives.org/ore/terms/}ResourceMap``.
ns_reverse... | python | def replace_namespace_with_prefix(tag_str, ns_reverse_dict=None):
"""Convert XML tag names with namespace on the form ``{namespace}tag`` to form
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Args:
tag_str: str
Tag name with namespace. E.g.:
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | etree_replace_namespace | def etree_replace_namespace(etree_obj, ns_str):
"""In-place change the namespace of elements in an ElementTree.
Args:
etree_obj: ElementTree
ns_str : str
The namespace to set. E.g.: ``http://ns.dataone.org/service/types/v1``.
"""
def _replace_recursive(el, n):
el.tag = re... | python | def etree_replace_namespace(etree_obj, ns_str):
"""In-place change the namespace of elements in an ElementTree.
Args:
etree_obj: ElementTree
ns_str : str
The namespace to set. E.g.: ``http://ns.dataone.org/service/types/v1``.
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | strip_v2_elements | def strip_v2_elements(etree_obj):
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Args: etree_obj: ElementTree ElementTree holding one of the DataONE API types
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"""
if etree_obj.tag == v2_0_tag('logEntry'):
strip_logEntry(etr... | python | def strip_v2_elements(etree_obj):
"""In-place remove elements and attributes that are only valid in v2 types.
Args: etree_obj: ElementTree ElementTree holding one of the DataONE API types
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DataONEorg/d1_python | lib_common/src/d1_common/type_conversions.py | strip_system_metadata | def strip_system_metadata(etree_obj):
"""In-place remove elements and attributes that are only valid in v2 types from v1
System Metadata.
Args: etree_obj: ElementTree ElementTree holding a v1 SystemMetadata.
"""
for series_id_el in etree_obj.findall('seriesId'):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/process_replication_queue.py | ReplicationQueueProcessor._create_replica | def _create_replica(self, sysmeta_pyxb, sciobj_bytestream):
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So this create sequence differs significantly from the regular on... | python | def _create_replica(self, sysmeta_pyxb, sciobj_bytestream):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.restricted_import | async def restricted_import(self, async_client, node_type):
"""Import only the Science Objects specified by a text file.
The file must be UTF-8 encoded and contain one PIDs or SIDs per line.
"""
item_task_name = "Importing objects"
pid_path = self.options['pid_path']
i... | python | async def restricted_import(self, async_client, node_type):
"""Import only the Science Objects specified by a text file.
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item_task_name = "Importing objects"
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.import_aggregated | async def import_aggregated(self, async_client, pid):
"""Import the SciObj at {pid}.
If the SciObj is a Resource Map, also recursively import the aggregated objects.
"""
self._logger.info('Importing: {}'.format(pid))
task_set = set()
object_info_pyxb = d1_common.types... | python | async def import_aggregated(self, async_client, pid):
"""Import the SciObj at {pid}.
If the SciObj is a Resource Map, also recursively import the aggregated objects.
"""
self._logger.info('Importing: {}'.format(pid))
task_set = set()
object_info_pyxb = d1_common.types... | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.get_object_proxy_location | async def get_object_proxy_location(self, client, pid):
"""If object is proxied, return the proxy location URL.
If object is local, return None.
"""
try:
return (await client.describe(pid)).get("DataONE-Proxy")
except d1_common.types.exceptions.DataONEException:
... | python | async def get_object_proxy_location(self, client, pid):
"""If object is proxied, return the proxy location URL.
If object is local, return None.
"""
try:
return (await client.describe(pid)).get("DataONE-Proxy")
except d1_common.types.exceptions.DataONEException:
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.get_list_objects_arg_dict | def get_list_objects_arg_dict(self, node_type):
"""Create a dict of arguments that will be passed to listObjects().
If {node_type} is a CN, add filtering to include only objects from this GMN
instance in the ObjectList returned by CNCore.listObjects().
"""
arg_dict = {
... | python | def get_list_objects_arg_dict(self, node_type):
"""Create a dict of arguments that will be passed to listObjects().
If {node_type} is a CN, add filtering to include only objects from this GMN
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arg_dict = {
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.get_log_records_arg_dict | def get_log_records_arg_dict(self, node_type):
"""Create a dict of arguments that will be passed to getLogRecords().
If {node_type} is a CN, add filtering to include only objects from this GMN
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"""
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"""Create a dict of arguments that will be passed to getLogRecords().
If {node_type} is a CN, add filtering to include only objects from this GMN
instance in the ObjectList returned by CNCore.listObjects().
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.is_cn | async def is_cn(self, client):
"""Return True if node at {base_url} is a CN, False if it is an MN.
Raise a DataONEException if it's not a functional CN or MN.
"""
node_pyxb = await client.get_capabilities()
return d1_common.type_conversions.pyxb_get_type_name(node_pyxb) == "Nod... | python | async def is_cn(self, client):
"""Return True if node at {base_url} is a CN, False if it is an MN.
Raise a DataONEException if it's not a functional CN or MN.
"""
node_pyxb = await client.get_capabilities()
return d1_common.type_conversions.pyxb_get_type_name(node_pyxb) == "Nod... | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.probe_node_type_major | async def probe_node_type_major(self, client):
"""Determine if import source node is a CN or MN and which major version API to
use."""
try:
node_pyxb = await self.get_node_doc(client)
except d1_common.types.exceptions.DataONEException as e:
raise django.core.manag... | python | async def probe_node_type_major(self, client):
"""Determine if import source node is a CN or MN and which major version API to
use."""
try:
node_pyxb = await self.get_node_doc(client)
except d1_common.types.exceptions.DataONEException as e:
raise django.core.manag... | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.find_node | def find_node(self, node_list_pyxb, base_url):
"""Search NodeList for Node that has {base_url}.
Return matching Node or None
"""
for node_pyxb in node_list_pyxb.node:
if node_pyxb.baseURL == base_url:
return node_pyxb | python | def find_node(self, node_list_pyxb, base_url):
"""Search NodeList for Node that has {base_url}.
Return matching Node or None
"""
for node_pyxb in node_list_pyxb.node:
if node_pyxb.baseURL == base_url:
return node_pyxb | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.assert_is_known_node_id | def assert_is_known_node_id(self, node_list_pyxb, node_id):
"""When importing from a CN, ensure that the NodeID which the ObjectList will be
filtered by is known to the CN."""
node_pyxb = self.find_node_by_id(node_list_pyxb, node_id)
assert node_pyxb is not None, (
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"""When importing from a CN, ensure that the NodeID which the ObjectList will be
filtered by is known to the CN."""
node_pyxb = self.find_node_by_id(node_list_pyxb, node_id)
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.find_node_api_version | def find_node_api_version(self, node_pyxb):
"""Find the highest API major version supported by node."""
max_major = 0
for s in node_pyxb.services.service:
max_major = max(max_major, int(s.version[1:]))
return max_major | python | def find_node_api_version(self, node_pyxb):
"""Find the highest API major version supported by node."""
max_major = 0
for s in node_pyxb.services.service:
max_major = max(max_major, int(s.version[1:]))
return max_major | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import.py | Command.find_node_by_id | def find_node_by_id(self, node_list_pyxb, node_id):
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Return matching Node or None
"""
for node_pyxb in node_list_pyxb.node:
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"""Search NodeList for Node with {node_id}.
Return matching Node or None
"""
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genialis/resolwe | resolwe/flow/tasks.py | celery_run | def celery_run(data_id, runtime_dir, argv):
"""Run process executor.
:param data_id: The id of the :class:`~resolwe.flow.models.Data`
object to be processed.
:param runtime_dir: The directory from which to run the executor.
:param argv: The argument vector used to run the executor.
:param v... | python | def celery_run(data_id, runtime_dir, argv):
"""Run process executor.
:param data_id: The id of the :class:`~resolwe.flow.models.Data`
object to be processed.
:param runtime_dir: The directory from which to run the executor.
:param argv: The argument vector used to run the executor.
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta.py | archive_sciobj | def archive_sciobj(pid):
"""Set the status of an object to archived.
Preconditions:
- The object with the pid is verified to exist.
- The object is not a replica.
- The object is not archived.
"""
sciobj_model = d1_gmn.app.model_util.get_sci_model(pid)
sciobj_model.is_archived = True
... | python | def archive_sciobj(pid):
"""Set the status of an object to archived.
Preconditions:
- The object with the pid is verified to exist.
- The object is not a replica.
- The object is not archived.
"""
sciobj_model = d1_gmn.app.model_util.get_sci_model(pid)
sciobj_model.is_archived = True
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta.py | create_or_update | def create_or_update(sysmeta_pyxb, sciobj_url=None):
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related internal state.
- If ``sciobj_url`` is not passed on create, storage in the internal sciobj store
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- If ``sciobj_url`` is passed on create, it... | python | def create_or_update(sysmeta_pyxb, sciobj_url=None):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/sysmeta.py | _access_policy_pyxb_to_model | def _access_policy_pyxb_to_model(sci_model, sysmeta_pyxb):
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import-multiprocess.py | Command.add_arguments | def add_arguments(self, parser):
"""Args:
parser:
"""
parser.description = __doc__
parser.formatter_class = argparse.RawDescriptionHelpFormatter
parser.add_argument("--debug", action="store_true", help="Debug level logging")
parser.add_argument(
"--f... | python | def add_arguments(self, parser):
"""Args:
parser:
"""
parser.description = __doc__
parser.formatter_class = argparse.RawDescriptionHelpFormatter
parser.add_argument("--debug", action="store_true", help="Debug level logging")
parser.add_argument(
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import-multiprocess.py | Command.handle | def handle(self, *args, **opt):
"""Args:
*args:
**opt:
"""
d1_gmn.app.management.commands.util.util.log_setup(opt["debug"])
logging.info(
"Running management command: {}".format(
__name__
) # util.get_command_name())
)
... | python | def handle(self, *args, **opt):
"""Args:
*args:
**opt:
"""
d1_gmn.app.management.commands.util.util.log_setup(opt["debug"])
logging.info(
"Running management command: {}".format(
__name__
) # util.get_command_name())
)
... | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import-multiprocess.py | Command._create_log_entry | def _create_log_entry(self, log_record_pyxb):
"""Args:
log_record_pyxb:
"""
event_log_model = d1_gmn.app.event_log.create_log_entry(
d1_gmn.app.model_util.get_sci_model(
d1_common.xml.get_req_val(log_record_pyxb.identifier)
),
log_rec... | python | def _create_log_entry(self, log_record_pyxb):
"""Args:
log_record_pyxb:
"""
event_log_model = d1_gmn.app.event_log.create_log_entry(
d1_gmn.app.model_util.get_sci_model(
d1_common.xml.get_req_val(log_record_pyxb.identifier)
),
log_rec... | [
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import-multiprocess.py | Command._download_source_sciobj_bytes_to_store | def _download_source_sciobj_bytes_to_store(self, client, pid):
"""Args:
client: pid:
"""
if d1_gmn.app.sciobj_store.is_existing_sciobj_file(pid):
self._events.log_and_count(
"Skipped download of existing sciobj bytes", 'pid="{}"'.format(pid)
)
... | python | def _download_source_sciobj_bytes_to_store(self, client, pid):
"""Args:
client: pid:
"""
if d1_gmn.app.sciobj_store.is_existing_sciobj_file(pid):
self._events.log_and_count(
"Skipped download of existing sciobj bytes", 'pid="{}"'.format(pid)
)
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DataONEorg/d1_python | gmn/src/d1_gmn/app/management/commands/import-multiprocess.py | Command._assert_path_is_dir | def _assert_path_is_dir(self, dir_path):
"""Args:
dir_path:
"""
if not os.path.isdir(dir_path):
raise django.core.management.base.CommandError(
'Invalid dir path. path="{}"'.format(dir_path)
) | python | def _assert_path_is_dir(self, dir_path):
"""Args:
dir_path:
"""
if not os.path.isdir(dir_path):
raise django.core.management.base.CommandError(
'Invalid dir path. path="{}"'.format(dir_path)
) | [
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DataONEorg/d1_python | lib_common/src/d1_common/cert/view_subject_info.py | deserialize_subject_info | def deserialize_subject_info(subject_info_xml_path):
"""Deserialize a SubjectInfo XML file to a PyXB object."""
try:
with open(subject_info_xml_path) as f:
return d1_common.xml.deserialize(f.read())
except ValueError as e:
raise d1_common.types.exceptions.InvalidToken(
... | python | def deserialize_subject_info(subject_info_xml_path):
"""Deserialize a SubjectInfo XML file to a PyXB object."""
try:
with open(subject_info_xml_path) as f:
return d1_common.xml.deserialize(f.read())
except ValueError as e:
raise d1_common.types.exceptions.InvalidToken(
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.HEAD | def HEAD(self, rest_path_list, **kwargs):
"""Send a HEAD request. See requests.sessions.request for optional parameters.
:returns: Response object
"""
kwargs.setdefault("allow_redirects", False)
return self._request("HEAD", rest_path_list, **kwargs) | python | def HEAD(self, rest_path_list, **kwargs):
"""Send a HEAD request. See requests.sessions.request for optional parameters.
:returns: Response object
"""
kwargs.setdefault("allow_redirects", False)
return self._request("HEAD", rest_path_list, **kwargs) | [
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.POST | def POST(self, rest_path_list, **kwargs):
"""Send a POST request with optional streaming multipart encoding. See
requests.sessions.request for optional parameters. To post regular data, pass a
string, iterator or generator as the ``data`` argument. To post a multipart
stream, pass a dict... | python | def POST(self, rest_path_list, **kwargs):
"""Send a POST request with optional streaming multipart encoding. See
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.PUT | def PUT(self, rest_path_list, **kwargs):
"""Send a PUT request with optional streaming multipart encoding. See
requests.sessions.request for optional parameters. See post() for parameters.
:returns: Response object
"""
fields = kwargs.pop("fields", None)
if fields is no... | python | def PUT(self, rest_path_list, **kwargs):
"""Send a PUT request with optional streaming multipart encoding. See
requests.sessions.request for optional parameters. See post() for parameters.
:returns: Response object
"""
fields = kwargs.pop("fields", None)
if fields is no... | [
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.get_curl_command_line | def get_curl_command_line(self, method, url, **kwargs):
"""Get request as cURL command line for debugging."""
if kwargs.get("query"):
url = "{}?{}".format(url, d1_common.url.urlencode(kwargs["query"]))
curl_list = ["curl"]
if method.lower() == "head":
curl_list.ap... | python | def get_curl_command_line(self, method, url, **kwargs):
"""Get request as cURL command line for debugging."""
if kwargs.get("query"):
url = "{}?{}".format(url, d1_common.url.urlencode(kwargs["query"]))
curl_list = ["curl"]
if method.lower() == "head":
curl_list.ap... | [
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DataONEorg/d1_python | lib_client/src/d1_client/session.py | Session.dump_request_and_response | def dump_request_and_response(self, response):
"""Return a string containing a nicely formatted representation of the request
and response objects for logging and debugging.
- Note: Does not work if the request or response body is a MultipartEncoder
object.
"""
if res... | python | def dump_request_and_response(self, response):
"""Return a string containing a nicely formatted representation of the request
and response objects for logging and debugging.
- Note: Does not work if the request or response body is a MultipartEncoder
object.
"""
if res... | [
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