id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
|---|---|---|---|---|---|---|---|---|---|---|---|
19,700 | chaoss/grimoirelab-elk | grimoire_elk/utils.py | get_time_diff_days | def get_time_diff_days(start_txt, end_txt):
''' Number of days between two days '''
if start_txt is None or end_txt is None:
return None
start = parser.parse(start_txt)
end = parser.parse(end_txt)
seconds_day = float(60 * 60 * 24)
diff_days = \
(end - start).total_seconds() / seconds_day
diff_days = float('%.2f' % diff_days)
return diff_days | python | def get_time_diff_days(start_txt, end_txt):
''' Number of days between two days '''
if start_txt is None or end_txt is None:
return None
start = parser.parse(start_txt)
end = parser.parse(end_txt)
seconds_day = float(60 * 60 * 24)
diff_days = \
(end - start).total_seconds() / seconds_day
diff_days = float('%.2f' % diff_days)
return diff_days | [
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19,701 | chaoss/grimoirelab-elk | grimoire_elk/enriched/jira.py | JiraEnrich.enrich_fields | def enrich_fields(cls, fields, eitem):
"""Enrich the fields property of an issue.
Loops through al properties in issue['fields'],
using those that are relevant to enrich eitem with new properties.
Those properties are user defined, depending on options
configured in Jira. For example, if SCRUM is activated,
we have a field named "Story Points".
:param fields: fields property of an issue
:param eitem: enriched item, which will be modified adding more properties
"""
for field in fields:
if field.startswith('customfield_'):
if type(fields[field]) is dict:
if 'name' in fields[field]:
if fields[field]['name'] == "Story Points":
eitem['story_points'] = fields[field]['value']
elif fields[field]['name'] == "Sprint":
value = fields[field]['value']
if value:
sprint = value[0].partition(",name=")[2].split(',')[0]
sprint_start = value[0].partition(",startDate=")[2].split(',')[0]
sprint_end = value[0].partition(",endDate=")[2].split(',')[0]
sprint_complete = value[0].partition(",completeDate=")[2].split(',')[0]
eitem['sprint'] = sprint
eitem['sprint_start'] = cls.fix_value_null(sprint_start)
eitem['sprint_end'] = cls.fix_value_null(sprint_end)
eitem['sprint_complete'] = cls.fix_value_null(sprint_complete) | python | def enrich_fields(cls, fields, eitem):
for field in fields:
if field.startswith('customfield_'):
if type(fields[field]) is dict:
if 'name' in fields[field]:
if fields[field]['name'] == "Story Points":
eitem['story_points'] = fields[field]['value']
elif fields[field]['name'] == "Sprint":
value = fields[field]['value']
if value:
sprint = value[0].partition(",name=")[2].split(',')[0]
sprint_start = value[0].partition(",startDate=")[2].split(',')[0]
sprint_end = value[0].partition(",endDate=")[2].split(',')[0]
sprint_complete = value[0].partition(",completeDate=")[2].split(',')[0]
eitem['sprint'] = sprint
eitem['sprint_start'] = cls.fix_value_null(sprint_start)
eitem['sprint_end'] = cls.fix_value_null(sprint_end)
eitem['sprint_complete'] = cls.fix_value_null(sprint_complete) | [
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19,702 | chaoss/grimoirelab-elk | grimoire_elk/enriched/mediawiki.py | MediaWikiEnrich.get_review_sh | def get_review_sh(self, revision, item):
""" Add sorting hat enrichment fields for the author of the revision """
identity = self.get_sh_identity(revision)
update = parser.parse(item[self.get_field_date()])
erevision = self.get_item_sh_fields(identity, update)
return erevision | python | def get_review_sh(self, revision, item):
identity = self.get_sh_identity(revision)
update = parser.parse(item[self.get_field_date()])
erevision = self.get_item_sh_fields(identity, update)
return erevision | [
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19,703 | chaoss/grimoirelab-elk | grimoire_elk/enriched/github.py | GitHubEnrich.get_github_cache | def get_github_cache(self, kind, key_):
""" Get cache data for items of _type using key_ as the cache dict key """
cache = {}
res_size = 100 # best size?
from_ = 0
index_github = "github/" + kind
url = self.elastic.url + "/" + index_github
url += "/_search" + "?" + "size=%i" % res_size
r = self.requests.get(url)
type_items = r.json()
if 'hits' not in type_items:
logger.info("No github %s data in ES" % (kind))
else:
while len(type_items['hits']['hits']) > 0:
for hit in type_items['hits']['hits']:
item = hit['_source']
cache[item[key_]] = item
from_ += res_size
r = self.requests.get(url + "&from=%i" % from_)
type_items = r.json()
if 'hits' not in type_items:
break
return cache | python | def get_github_cache(self, kind, key_):
cache = {}
res_size = 100 # best size?
from_ = 0
index_github = "github/" + kind
url = self.elastic.url + "/" + index_github
url += "/_search" + "?" + "size=%i" % res_size
r = self.requests.get(url)
type_items = r.json()
if 'hits' not in type_items:
logger.info("No github %s data in ES" % (kind))
else:
while len(type_items['hits']['hits']) > 0:
for hit in type_items['hits']['hits']:
item = hit['_source']
cache[item[key_]] = item
from_ += res_size
r = self.requests.get(url + "&from=%i" % from_)
type_items = r.json()
if 'hits' not in type_items:
break
return cache | [
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19,704 | chaoss/grimoirelab-elk | grimoire_elk/enriched/github.py | GitHubEnrich.get_time_to_first_attention | def get_time_to_first_attention(self, item):
"""Get the first date at which a comment or reaction was made to the issue by someone
other than the user who created the issue
"""
comment_dates = [str_to_datetime(comment['created_at']) for comment in item['comments_data']
if item['user']['login'] != comment['user']['login']]
reaction_dates = [str_to_datetime(reaction['created_at']) for reaction in item['reactions_data']
if item['user']['login'] != reaction['user']['login']]
reaction_dates.extend(comment_dates)
if reaction_dates:
return min(reaction_dates)
return None | python | def get_time_to_first_attention(self, item):
comment_dates = [str_to_datetime(comment['created_at']) for comment in item['comments_data']
if item['user']['login'] != comment['user']['login']]
reaction_dates = [str_to_datetime(reaction['created_at']) for reaction in item['reactions_data']
if item['user']['login'] != reaction['user']['login']]
reaction_dates.extend(comment_dates)
if reaction_dates:
return min(reaction_dates)
return None | [
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19,705 | chaoss/grimoirelab-elk | grimoire_elk/enriched/github.py | GitHubEnrich.get_time_to_merge_request_response | def get_time_to_merge_request_response(self, item):
"""Get the first date at which a review was made on the PR by someone
other than the user who created the PR
"""
review_dates = [str_to_datetime(review['created_at']) for review in item['review_comments_data']
if item['user']['login'] != review['user']['login']]
if review_dates:
return min(review_dates)
return None | python | def get_time_to_merge_request_response(self, item):
review_dates = [str_to_datetime(review['created_at']) for review in item['review_comments_data']
if item['user']['login'] != review['user']['login']]
if review_dates:
return min(review_dates)
return None | [
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19,706 | chaoss/grimoirelab-elk | grimoire_elk/enriched/crates.py | CratesEnrich.get_rich_events | def get_rich_events(self, item):
"""
In the events there are some common fields with the crate. The name
of the field must be the same in the create and in the downloads event
so we can filer using it in crate and event at the same time.
* Fields that don't change: the field does not change with the events
in a create so the value is always the same in the events of a create.
* Fields that change: the value of the field changes with events
"""
if "version_downloads_data" not in item['data']:
return []
# To get values from the task
eitem = self.get_rich_item(item)
for sample in item['data']["version_downloads_data"]["version_downloads"]:
event = deepcopy(eitem)
event['download_sample_id'] = sample['id']
event['sample_date'] = sample['date']
sample_date = parser.parse(event['sample_date'])
event['sample_version'] = sample['version']
event['sample_downloads'] = sample['downloads']
event.update(self.get_grimoire_fields(sample_date.isoformat(), "downloads_event"))
yield event | python | def get_rich_events(self, item):
if "version_downloads_data" not in item['data']:
return []
# To get values from the task
eitem = self.get_rich_item(item)
for sample in item['data']["version_downloads_data"]["version_downloads"]:
event = deepcopy(eitem)
event['download_sample_id'] = sample['id']
event['sample_date'] = sample['date']
sample_date = parser.parse(event['sample_date'])
event['sample_version'] = sample['version']
event['sample_downloads'] = sample['downloads']
event.update(self.get_grimoire_fields(sample_date.isoformat(), "downloads_event"))
yield event | [
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19,707 | chaoss/grimoirelab-elk | grimoire_elk/enriched/twitter.py | TwitterEnrich.get_item_project | def get_item_project(self, eitem):
""" Get project mapping enrichment field.
Twitter mappings is pretty special so it needs a special
implementacion.
"""
project = None
eitem_project = {}
ds_name = self.get_connector_name() # data source name in projects map
if ds_name not in self.prjs_map:
return eitem_project
for tag in eitem['hashtags_analyzed']:
# lcanas: hashtag provided in projects.json file should not be case sensitive T6876
tags2project = CaseInsensitiveDict(self.prjs_map[ds_name])
if tag in tags2project:
project = tags2project[tag]
break
if project is None:
project = DEFAULT_PROJECT
eitem_project = {"project": project}
eitem_project.update(self.add_project_levels(project))
return eitem_project | python | def get_item_project(self, eitem):
project = None
eitem_project = {}
ds_name = self.get_connector_name() # data source name in projects map
if ds_name not in self.prjs_map:
return eitem_project
for tag in eitem['hashtags_analyzed']:
# lcanas: hashtag provided in projects.json file should not be case sensitive T6876
tags2project = CaseInsensitiveDict(self.prjs_map[ds_name])
if tag in tags2project:
project = tags2project[tag]
break
if project is None:
project = DEFAULT_PROJECT
eitem_project = {"project": project}
eitem_project.update(self.add_project_levels(project))
return eitem_project | [
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19,708 | chaoss/grimoirelab-elk | grimoire_elk/enriched/jenkins.py | JenkinsEnrich.get_fields_from_job_name | def get_fields_from_job_name(self, job_name):
"""Analyze a Jenkins job name, producing a dictionary
The produced dictionary will include information about the category
and subcategory of the job name, and any extra information which
could be useful.
For each deployment of a Jenkins dashboard, an implementation of
this function should be produced, according to the needs of the users.
:param job: job name to Analyze
:returns: dictionary with categorization information
"""
extra_fields = {
'category': None,
'installer': None,
'scenario': None,
'testproject': None,
'pod': None,
'loop': None,
'branch': None
}
try:
components = job_name.split('-')
if len(components) < 2:
return extra_fields
kind = components[1]
if kind == 'os':
extra_fields['category'] = 'parent/main'
extra_fields['installer'] = components[0]
extra_fields['scenario'] = '-'.join(components[2:-3])
elif kind == 'deploy':
extra_fields['category'] = 'deploy'
extra_fields['installer'] = components[0]
else:
extra_fields['category'] = 'test'
extra_fields['testproject'] = components[0]
extra_fields['installer'] = components[1]
extra_fields['pod'] = components[-3]
extra_fields['loop'] = components[-2]
extra_fields['branch'] = components[-1]
except IndexError as ex:
# Just DEBUG level because it is just for OPNFV
logger.debug('Problems parsing job name %s', job_name)
logger.debug(ex)
return extra_fields | python | def get_fields_from_job_name(self, job_name):
extra_fields = {
'category': None,
'installer': None,
'scenario': None,
'testproject': None,
'pod': None,
'loop': None,
'branch': None
}
try:
components = job_name.split('-')
if len(components) < 2:
return extra_fields
kind = components[1]
if kind == 'os':
extra_fields['category'] = 'parent/main'
extra_fields['installer'] = components[0]
extra_fields['scenario'] = '-'.join(components[2:-3])
elif kind == 'deploy':
extra_fields['category'] = 'deploy'
extra_fields['installer'] = components[0]
else:
extra_fields['category'] = 'test'
extra_fields['testproject'] = components[0]
extra_fields['installer'] = components[1]
extra_fields['pod'] = components[-3]
extra_fields['loop'] = components[-2]
extra_fields['branch'] = components[-1]
except IndexError as ex:
# Just DEBUG level because it is just for OPNFV
logger.debug('Problems parsing job name %s', job_name)
logger.debug(ex)
return extra_fields | [
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19,709 | chaoss/grimoirelab-elk | grimoire_elk/enriched/jenkins.py | JenkinsEnrich.extract_builton | def extract_builton(self, built_on, regex):
"""Extracts node name using a regular expression. Node name is expected to
be group 1.
"""
pattern = re.compile(regex, re.M | re.I)
match = pattern.search(built_on)
if match and len(match.groups()) >= 1:
node_name = match.group(1)
else:
msg = "Node name not extracted, using builtOn as it is: " + regex + ":" + built_on
logger.warning(msg)
node_name = built_on
return node_name | python | def extract_builton(self, built_on, regex):
pattern = re.compile(regex, re.M | re.I)
match = pattern.search(built_on)
if match and len(match.groups()) >= 1:
node_name = match.group(1)
else:
msg = "Node name not extracted, using builtOn as it is: " + regex + ":" + built_on
logger.warning(msg)
node_name = built_on
return node_name | [
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19,710 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_onion.py | onion_study | def onion_study(in_conn, out_conn, data_source):
"""Build and index for onion from a given Git index.
:param in_conn: ESPandasConnector to read from.
:param out_conn: ESPandasConnector to write to.
:param data_source: name of the date source to generate onion from.
:return: number of documents written in ElasticSearch enriched index.
"""
onion = OnionStudy(in_connector=in_conn, out_connector=out_conn, data_source=data_source)
ndocs = onion.analyze()
return ndocs | python | def onion_study(in_conn, out_conn, data_source):
onion = OnionStudy(in_connector=in_conn, out_connector=out_conn, data_source=data_source)
ndocs = onion.analyze()
return ndocs | [
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19,711 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_onion.py | ESOnionConnector.read_block | def read_block(self, size=None, from_date=None):
"""Read author commits by Quarter, Org and Project.
:param from_date: not used here. Incremental mode not supported yet.
:param size: not used here.
:return: DataFrame with commit count per author, split by quarter, org and project.
"""
# Get quarters corresponding to All items (Incremental mode NOT SUPPORTED)
quarters = self.__quarters()
for quarter in quarters:
logger.info(self.__log_prefix + " Quarter: " + str(quarter))
date_range = {self._timeframe_field: {'gte': quarter.start_time, 'lte': quarter.end_time}}
orgs = self.__list_uniques(date_range, self.AUTHOR_ORG)
projects = self.__list_uniques(date_range, self.PROJECT)
# Get global data
s = self.__build_search(date_range)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing).copy()
# Get global data by Org
for org_name in orgs:
logger.info(self.__log_prefix + " Quarter: " + str(quarter) + " Org: " + org_name)
s = self.__build_search(date_range, org_name=org_name)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing, org_name=org_name).copy()
# Get project specific data
for project in projects:
logger.info(self.__log_prefix + " Quarter: " + str(quarter) + " Project: " + project)
# Global project
s = self.__build_search(date_range, project_name=project)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing, project_name=project).copy()
# Split by Org
for org_name in orgs:
logger.info(self.__log_prefix + " Quarter: " + str(quarter) + " Project: " + project + " Org: " + org_name)
s = self.__build_search(date_range, project_name=project, org_name=org_name)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing, project_name=project, org_name=org_name).copy() | python | def read_block(self, size=None, from_date=None):
# Get quarters corresponding to All items (Incremental mode NOT SUPPORTED)
quarters = self.__quarters()
for quarter in quarters:
logger.info(self.__log_prefix + " Quarter: " + str(quarter))
date_range = {self._timeframe_field: {'gte': quarter.start_time, 'lte': quarter.end_time}}
orgs = self.__list_uniques(date_range, self.AUTHOR_ORG)
projects = self.__list_uniques(date_range, self.PROJECT)
# Get global data
s = self.__build_search(date_range)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing).copy()
# Get global data by Org
for org_name in orgs:
logger.info(self.__log_prefix + " Quarter: " + str(quarter) + " Org: " + org_name)
s = self.__build_search(date_range, org_name=org_name)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing, org_name=org_name).copy()
# Get project specific data
for project in projects:
logger.info(self.__log_prefix + " Quarter: " + str(quarter) + " Project: " + project)
# Global project
s = self.__build_search(date_range, project_name=project)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing, project_name=project).copy()
# Split by Org
for org_name in orgs:
logger.info(self.__log_prefix + " Quarter: " + str(quarter) + " Project: " + project + " Org: " + org_name)
s = self.__build_search(date_range, project_name=project, org_name=org_name)
response = s.execute()
for timing in response.aggregations[self.TIMEFRAME].buckets:
yield self.__build_dataframe(timing, project_name=project, org_name=org_name).copy() | [
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19,712 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_onion.py | ESOnionConnector.__quarters | def __quarters(self, from_date=None):
"""Get a set of quarters with available items from a given index date.
:param from_date:
:return: list of `pandas.Period` corresponding to quarters
"""
s = Search(using=self._es_conn, index=self._es_index)
if from_date:
# Work around to solve conversion problem of '__' to '.' in field name
q = Q('range')
q.__setattr__(self._sort_on_field, {'gte': from_date})
s = s.filter(q)
# from:to parameters (=> from: 0, size: 0)
s = s[0:0]
s.aggs.bucket(self.TIMEFRAME, 'date_histogram', field=self._timeframe_field,
interval='quarter', min_doc_count=1)
response = s.execute()
quarters = []
for quarter in response.aggregations[self.TIMEFRAME].buckets:
period = pandas.Period(quarter.key_as_string, 'Q')
quarters.append(period)
return quarters | python | def __quarters(self, from_date=None):
s = Search(using=self._es_conn, index=self._es_index)
if from_date:
# Work around to solve conversion problem of '__' to '.' in field name
q = Q('range')
q.__setattr__(self._sort_on_field, {'gte': from_date})
s = s.filter(q)
# from:to parameters (=> from: 0, size: 0)
s = s[0:0]
s.aggs.bucket(self.TIMEFRAME, 'date_histogram', field=self._timeframe_field,
interval='quarter', min_doc_count=1)
response = s.execute()
quarters = []
for quarter in response.aggregations[self.TIMEFRAME].buckets:
period = pandas.Period(quarter.key_as_string, 'Q')
quarters.append(period)
return quarters | [
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19,713 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_onion.py | ESOnionConnector.__list_uniques | def __list_uniques(self, date_range, field_name):
"""Retrieve a list of unique values in a given field within a date range.
:param date_range:
:param field_name:
:return: list of unique values.
"""
# Get project list
s = Search(using=self._es_conn, index=self._es_index)
s = s.filter('range', **date_range)
# from:to parameters (=> from: 0, size: 0)
s = s[0:0]
s.aggs.bucket('uniques', 'terms', field=field_name, size=1000)
response = s.execute()
uniques_list = []
for item in response.aggregations.uniques.buckets:
uniques_list.append(item.key)
return uniques_list | python | def __list_uniques(self, date_range, field_name):
# Get project list
s = Search(using=self._es_conn, index=self._es_index)
s = s.filter('range', **date_range)
# from:to parameters (=> from: 0, size: 0)
s = s[0:0]
s.aggs.bucket('uniques', 'terms', field=field_name, size=1000)
response = s.execute()
uniques_list = []
for item in response.aggregations.uniques.buckets:
uniques_list.append(item.key)
return uniques_list | [
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19,714 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_onion.py | ESOnionConnector.__build_dataframe | def __build_dataframe(self, timing, project_name=None, org_name=None):
"""Build a DataFrame from a time bucket.
:param timing:
:param project_name:
:param org_name:
:return:
"""
date_list = []
uuid_list = []
name_list = []
contribs_list = []
latest_ts_list = []
logger.debug(self.__log_prefix + " timing: " + timing.key_as_string)
for author in timing[self.AUTHOR_UUID].buckets:
latest_ts_list.append(timing[self.LATEST_TS].value_as_string)
date_list.append(timing.key_as_string)
uuid_list.append(author.key)
if author[self.AUTHOR_NAME] and author[self.AUTHOR_NAME].buckets \
and len(author[self.AUTHOR_NAME].buckets) > 0:
name_list.append(author[self.AUTHOR_NAME].buckets[0].key)
else:
name_list.append("Unknown")
contribs_list.append(author[self.CONTRIBUTIONS].value)
df = pandas.DataFrame()
df[self.TIMEFRAME] = date_list
df[self.AUTHOR_UUID] = uuid_list
df[self.AUTHOR_NAME] = name_list
df[self.CONTRIBUTIONS] = contribs_list
df[self.TIMESTAMP] = latest_ts_list
if not project_name:
project_name = "_Global_"
df[self.PROJECT] = project_name
if not org_name:
org_name = "_Global_"
df[self.AUTHOR_ORG] = org_name
return df | python | def __build_dataframe(self, timing, project_name=None, org_name=None):
date_list = []
uuid_list = []
name_list = []
contribs_list = []
latest_ts_list = []
logger.debug(self.__log_prefix + " timing: " + timing.key_as_string)
for author in timing[self.AUTHOR_UUID].buckets:
latest_ts_list.append(timing[self.LATEST_TS].value_as_string)
date_list.append(timing.key_as_string)
uuid_list.append(author.key)
if author[self.AUTHOR_NAME] and author[self.AUTHOR_NAME].buckets \
and len(author[self.AUTHOR_NAME].buckets) > 0:
name_list.append(author[self.AUTHOR_NAME].buckets[0].key)
else:
name_list.append("Unknown")
contribs_list.append(author[self.CONTRIBUTIONS].value)
df = pandas.DataFrame()
df[self.TIMEFRAME] = date_list
df[self.AUTHOR_UUID] = uuid_list
df[self.AUTHOR_NAME] = name_list
df[self.CONTRIBUTIONS] = contribs_list
df[self.TIMESTAMP] = latest_ts_list
if not project_name:
project_name = "_Global_"
df[self.PROJECT] = project_name
if not org_name:
org_name = "_Global_"
df[self.AUTHOR_ORG] = org_name
return df | [
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19,715 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_onion.py | OnionStudy.process | def process(self, items_block):
"""Process a DataFrame to compute Onion.
:param items_block: items to be processed. Expects to find a pandas DataFrame.
"""
logger.info(self.__log_prefix + " Authors to process: " + str(len(items_block)))
onion_enrich = Onion(items_block)
df_onion = onion_enrich.enrich(member_column=ESOnionConnector.AUTHOR_UUID,
events_column=ESOnionConnector.CONTRIBUTIONS)
# Get and store Quarter as String
df_onion['quarter'] = df_onion[ESOnionConnector.TIMEFRAME].map(lambda x: str(pandas.Period(x, 'Q')))
# Add metadata: enriched on timestamp
df_onion['metadata__enriched_on'] = datetime.utcnow().isoformat()
df_onion['data_source'] = self.data_source
df_onion['grimoire_creation_date'] = df_onion[ESOnionConnector.TIMEFRAME]
logger.info(self.__log_prefix + " Final new events: " + str(len(df_onion)))
return self.ProcessResults(processed=len(df_onion), out_items=df_onion) | python | def process(self, items_block):
logger.info(self.__log_prefix + " Authors to process: " + str(len(items_block)))
onion_enrich = Onion(items_block)
df_onion = onion_enrich.enrich(member_column=ESOnionConnector.AUTHOR_UUID,
events_column=ESOnionConnector.CONTRIBUTIONS)
# Get and store Quarter as String
df_onion['quarter'] = df_onion[ESOnionConnector.TIMEFRAME].map(lambda x: str(pandas.Period(x, 'Q')))
# Add metadata: enriched on timestamp
df_onion['metadata__enriched_on'] = datetime.utcnow().isoformat()
df_onion['data_source'] = self.data_source
df_onion['grimoire_creation_date'] = df_onion[ESOnionConnector.TIMEFRAME]
logger.info(self.__log_prefix + " Final new events: " + str(len(df_onion)))
return self.ProcessResults(processed=len(df_onion), out_items=df_onion) | [
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19,716 | chaoss/grimoirelab-elk | grimoire_elk/enriched/projects.py | GrimoireLibProjects.get_projects | def get_projects(self):
""" Get the projects list from database """
repos_list = []
gerrit_projects_db = self.projects_db
db = Database(user="root", passwd="", host="localhost", port=3306,
scrdb=None, shdb=gerrit_projects_db, prjdb=None)
sql = """
SELECT DISTINCT(repository_name)
FROM project_repositories
WHERE data_source='scr'
"""
repos_list_raw = db.execute(sql)
# Convert from review.openstack.org_openstack/rpm-packaging-tools to
# openstack_rpm-packaging-tools
for repo in repos_list_raw:
# repo_name = repo[0].replace("review.openstack.org_","")
repo_name = repo[0].replace(self.repository + "_", "")
repos_list.append(repo_name)
return repos_list | python | def get_projects(self):
repos_list = []
gerrit_projects_db = self.projects_db
db = Database(user="root", passwd="", host="localhost", port=3306,
scrdb=None, shdb=gerrit_projects_db, prjdb=None)
sql = """
SELECT DISTINCT(repository_name)
FROM project_repositories
WHERE data_source='scr'
"""
repos_list_raw = db.execute(sql)
# Convert from review.openstack.org_openstack/rpm-packaging-tools to
# openstack_rpm-packaging-tools
for repo in repos_list_raw:
# repo_name = repo[0].replace("review.openstack.org_","")
repo_name = repo[0].replace(self.repository + "_", "")
repos_list.append(repo_name)
return repos_list | [
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19,717 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | metadata | def metadata(func):
"""Add metadata to an item.
Decorator that adds metadata to a given item such as
the gelk revision used.
"""
@functools.wraps(func)
def decorator(self, *args, **kwargs):
eitem = func(self, *args, **kwargs)
metadata = {
'metadata__gelk_version': self.gelk_version,
'metadata__gelk_backend_name': self.__class__.__name__,
'metadata__enriched_on': datetime_utcnow().isoformat()
}
eitem.update(metadata)
return eitem
return decorator | python | def metadata(func):
@functools.wraps(func)
def decorator(self, *args, **kwargs):
eitem = func(self, *args, **kwargs)
metadata = {
'metadata__gelk_version': self.gelk_version,
'metadata__gelk_backend_name': self.__class__.__name__,
'metadata__enriched_on': datetime_utcnow().isoformat()
}
eitem.update(metadata)
return eitem
return decorator | [
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] | 64e08b324b36d9f6909bf705145d6451c8d34e65 | https://github.com/chaoss/grimoirelab-elk/blob/64e08b324b36d9f6909bf705145d6451c8d34e65/grimoire_elk/enriched/enrich.py#L78-L95 |
19,718 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.get_grimoire_fields | def get_grimoire_fields(self, creation_date, item_name):
""" Return common grimoire fields for all data sources """
grimoire_date = None
try:
grimoire_date = str_to_datetime(creation_date).isoformat()
except Exception as ex:
pass
name = "is_" + self.get_connector_name() + "_" + item_name
return {
"grimoire_creation_date": grimoire_date,
name: 1
} | python | def get_grimoire_fields(self, creation_date, item_name):
grimoire_date = None
try:
grimoire_date = str_to_datetime(creation_date).isoformat()
except Exception as ex:
pass
name = "is_" + self.get_connector_name() + "_" + item_name
return {
"grimoire_creation_date": grimoire_date,
name: 1
} | [
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19,719 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.add_project_levels | def add_project_levels(cls, project):
""" Add project sub levels extra items """
eitem_path = ''
eitem_project_levels = {}
if project is not None:
subprojects = project.split('.')
for i in range(0, len(subprojects)):
if i > 0:
eitem_path += "."
eitem_path += subprojects[i]
eitem_project_levels['project_' + str(i + 1)] = eitem_path
return eitem_project_levels | python | def add_project_levels(cls, project):
eitem_path = ''
eitem_project_levels = {}
if project is not None:
subprojects = project.split('.')
for i in range(0, len(subprojects)):
if i > 0:
eitem_path += "."
eitem_path += subprojects[i]
eitem_project_levels['project_' + str(i + 1)] = eitem_path
return eitem_project_levels | [
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19,720 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.get_item_metadata | def get_item_metadata(self, eitem):
"""
In the projects.json file, inside each project, there is a field called "meta" which has a
dictionary with fields to be added to the enriched items for this project.
This fields must be added with the prefix cm_ (custom metadata).
This method fetch the metadata fields for the project in which the eitem is included.
:param eitem: enriched item to search metadata for
:return: a dictionary with the metadata fields
"""
eitem_metadata = {}
# Get the project entry for the item, which includes the metadata
project = self.find_item_project(eitem)
if project and 'meta' in self.json_projects[project]:
meta_fields = self.json_projects[project]['meta']
if isinstance(meta_fields, dict):
eitem_metadata = {CUSTOM_META_PREFIX + "_" + field: value for field, value in meta_fields.items()}
return eitem_metadata | python | def get_item_metadata(self, eitem):
eitem_metadata = {}
# Get the project entry for the item, which includes the metadata
project = self.find_item_project(eitem)
if project and 'meta' in self.json_projects[project]:
meta_fields = self.json_projects[project]['meta']
if isinstance(meta_fields, dict):
eitem_metadata = {CUSTOM_META_PREFIX + "_" + field: value for field, value in meta_fields.items()}
return eitem_metadata | [
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This fields must be added with the prefix cm_ (custom metadata).
This method fetch the metadata fields for the project in which the eitem is included.
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:return: a dictionary with the metadata fields | [
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19,721 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.get_domain | def get_domain(self, identity):
""" Get the domain from a SH identity """
domain = None
if identity['email']:
try:
domain = identity['email'].split("@")[1]
except IndexError:
# logger.warning("Bad email format: %s" % (identity['email']))
pass
return domain | python | def get_domain(self, identity):
domain = None
if identity['email']:
try:
domain = identity['email'].split("@")[1]
except IndexError:
# logger.warning("Bad email format: %s" % (identity['email']))
pass
return domain | [
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19,722 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.get_enrollment | def get_enrollment(self, uuid, item_date):
""" Get the enrollment for the uuid when the item was done """
# item_date must be offset-naive (utc)
if item_date and item_date.tzinfo:
item_date = (item_date - item_date.utcoffset()).replace(tzinfo=None)
enrollments = self.get_enrollments(uuid)
enroll = self.unaffiliated_group
if enrollments:
for enrollment in enrollments:
if not item_date:
enroll = enrollment.organization.name
break
elif item_date >= enrollment.start and item_date <= enrollment.end:
enroll = enrollment.organization.name
break
return enroll | python | def get_enrollment(self, uuid, item_date):
# item_date must be offset-naive (utc)
if item_date and item_date.tzinfo:
item_date = (item_date - item_date.utcoffset()).replace(tzinfo=None)
enrollments = self.get_enrollments(uuid)
enroll = self.unaffiliated_group
if enrollments:
for enrollment in enrollments:
if not item_date:
enroll = enrollment.organization.name
break
elif item_date >= enrollment.start and item_date <= enrollment.end:
enroll = enrollment.organization.name
break
return enroll | [
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19,723 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.__get_item_sh_fields_empty | def __get_item_sh_fields_empty(self, rol, undefined=False):
""" Return a SH identity with all fields to empty_field """
# If empty_field is None, the fields do not appear in index patterns
empty_field = '' if not undefined else '-- UNDEFINED --'
return {
rol + "_id": empty_field,
rol + "_uuid": empty_field,
rol + "_name": empty_field,
rol + "_user_name": empty_field,
rol + "_domain": empty_field,
rol + "_gender": empty_field,
rol + "_gender_acc": None,
rol + "_org_name": empty_field,
rol + "_bot": False
} | python | def __get_item_sh_fields_empty(self, rol, undefined=False):
# If empty_field is None, the fields do not appear in index patterns
empty_field = '' if not undefined else '-- UNDEFINED --'
return {
rol + "_id": empty_field,
rol + "_uuid": empty_field,
rol + "_name": empty_field,
rol + "_user_name": empty_field,
rol + "_domain": empty_field,
rol + "_gender": empty_field,
rol + "_gender_acc": None,
rol + "_org_name": empty_field,
rol + "_bot": False
} | [
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19,724 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.get_item_sh_fields | def get_item_sh_fields(self, identity=None, item_date=None, sh_id=None,
rol='author'):
""" Get standard SH fields from a SH identity """
eitem_sh = self.__get_item_sh_fields_empty(rol)
if identity:
# Use the identity to get the SortingHat identity
sh_ids = self.get_sh_ids(identity, self.get_connector_name())
eitem_sh[rol + "_id"] = sh_ids.get('id', '')
eitem_sh[rol + "_uuid"] = sh_ids.get('uuid', '')
eitem_sh[rol + "_name"] = identity.get('name', '')
eitem_sh[rol + "_user_name"] = identity.get('username', '')
eitem_sh[rol + "_domain"] = self.get_identity_domain(identity)
elif sh_id:
# Use the SortingHat id to get the identity
eitem_sh[rol + "_id"] = sh_id
eitem_sh[rol + "_uuid"] = self.get_uuid_from_id(sh_id)
else:
# No data to get a SH identity. Return an empty one.
return eitem_sh
# If the identity does not exists return and empty identity
if rol + "_uuid" not in eitem_sh or not eitem_sh[rol + "_uuid"]:
return self.__get_item_sh_fields_empty(rol, undefined=True)
# Get the SH profile to use first this data
profile = self.get_profile_sh(eitem_sh[rol + "_uuid"])
if profile:
# If name not in profile, keep its old value (should be empty or identity's name field value)
eitem_sh[rol + "_name"] = profile.get('name', eitem_sh[rol + "_name"])
email = profile.get('email', None)
if email:
eitem_sh[rol + "_domain"] = self.get_email_domain(email)
eitem_sh[rol + "_gender"] = profile.get('gender', self.unknown_gender)
eitem_sh[rol + "_gender_acc"] = profile.get('gender_acc', 0)
elif not profile and sh_id:
logger.warning("Can't find SH identity profile: %s", sh_id)
# Ensure we always write gender fields
if not eitem_sh.get(rol + "_gender"):
eitem_sh[rol + "_gender"] = self.unknown_gender
eitem_sh[rol + "_gender_acc"] = 0
eitem_sh[rol + "_org_name"] = self.get_enrollment(eitem_sh[rol + "_uuid"], item_date)
eitem_sh[rol + "_bot"] = self.is_bot(eitem_sh[rol + '_uuid'])
return eitem_sh | python | def get_item_sh_fields(self, identity=None, item_date=None, sh_id=None,
rol='author'):
eitem_sh = self.__get_item_sh_fields_empty(rol)
if identity:
# Use the identity to get the SortingHat identity
sh_ids = self.get_sh_ids(identity, self.get_connector_name())
eitem_sh[rol + "_id"] = sh_ids.get('id', '')
eitem_sh[rol + "_uuid"] = sh_ids.get('uuid', '')
eitem_sh[rol + "_name"] = identity.get('name', '')
eitem_sh[rol + "_user_name"] = identity.get('username', '')
eitem_sh[rol + "_domain"] = self.get_identity_domain(identity)
elif sh_id:
# Use the SortingHat id to get the identity
eitem_sh[rol + "_id"] = sh_id
eitem_sh[rol + "_uuid"] = self.get_uuid_from_id(sh_id)
else:
# No data to get a SH identity. Return an empty one.
return eitem_sh
# If the identity does not exists return and empty identity
if rol + "_uuid" not in eitem_sh or not eitem_sh[rol + "_uuid"]:
return self.__get_item_sh_fields_empty(rol, undefined=True)
# Get the SH profile to use first this data
profile = self.get_profile_sh(eitem_sh[rol + "_uuid"])
if profile:
# If name not in profile, keep its old value (should be empty or identity's name field value)
eitem_sh[rol + "_name"] = profile.get('name', eitem_sh[rol + "_name"])
email = profile.get('email', None)
if email:
eitem_sh[rol + "_domain"] = self.get_email_domain(email)
eitem_sh[rol + "_gender"] = profile.get('gender', self.unknown_gender)
eitem_sh[rol + "_gender_acc"] = profile.get('gender_acc', 0)
elif not profile and sh_id:
logger.warning("Can't find SH identity profile: %s", sh_id)
# Ensure we always write gender fields
if not eitem_sh.get(rol + "_gender"):
eitem_sh[rol + "_gender"] = self.unknown_gender
eitem_sh[rol + "_gender_acc"] = 0
eitem_sh[rol + "_org_name"] = self.get_enrollment(eitem_sh[rol + "_uuid"], item_date)
eitem_sh[rol + "_bot"] = self.is_bot(eitem_sh[rol + '_uuid'])
return eitem_sh | [
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19,725 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.get_item_sh | def get_item_sh(self, item, roles=None, date_field=None):
"""
Add sorting hat enrichment fields for different roles
If there are no roles, just add the author fields.
"""
eitem_sh = {} # Item enriched
author_field = self.get_field_author()
if not roles:
roles = [author_field]
if not date_field:
item_date = str_to_datetime(item[self.get_field_date()])
else:
item_date = str_to_datetime(item[date_field])
users_data = self.get_users_data(item)
for rol in roles:
if rol in users_data:
identity = self.get_sh_identity(item, rol)
eitem_sh.update(self.get_item_sh_fields(identity, item_date, rol=rol))
if not eitem_sh[rol + '_org_name']:
eitem_sh[rol + '_org_name'] = SH_UNKNOWN_VALUE
if not eitem_sh[rol + '_name']:
eitem_sh[rol + '_name'] = SH_UNKNOWN_VALUE
if not eitem_sh[rol + '_user_name']:
eitem_sh[rol + '_user_name'] = SH_UNKNOWN_VALUE
# Add the author field common in all data sources
rol_author = 'author'
if author_field in users_data and author_field != rol_author:
identity = self.get_sh_identity(item, author_field)
eitem_sh.update(self.get_item_sh_fields(identity, item_date, rol=rol_author))
if not eitem_sh['author_org_name']:
eitem_sh['author_org_name'] = SH_UNKNOWN_VALUE
if not eitem_sh['author_name']:
eitem_sh['author_name'] = SH_UNKNOWN_VALUE
if not eitem_sh['author_user_name']:
eitem_sh['author_user_name'] = SH_UNKNOWN_VALUE
return eitem_sh | python | def get_item_sh(self, item, roles=None, date_field=None):
eitem_sh = {} # Item enriched
author_field = self.get_field_author()
if not roles:
roles = [author_field]
if not date_field:
item_date = str_to_datetime(item[self.get_field_date()])
else:
item_date = str_to_datetime(item[date_field])
users_data = self.get_users_data(item)
for rol in roles:
if rol in users_data:
identity = self.get_sh_identity(item, rol)
eitem_sh.update(self.get_item_sh_fields(identity, item_date, rol=rol))
if not eitem_sh[rol + '_org_name']:
eitem_sh[rol + '_org_name'] = SH_UNKNOWN_VALUE
if not eitem_sh[rol + '_name']:
eitem_sh[rol + '_name'] = SH_UNKNOWN_VALUE
if not eitem_sh[rol + '_user_name']:
eitem_sh[rol + '_user_name'] = SH_UNKNOWN_VALUE
# Add the author field common in all data sources
rol_author = 'author'
if author_field in users_data and author_field != rol_author:
identity = self.get_sh_identity(item, author_field)
eitem_sh.update(self.get_item_sh_fields(identity, item_date, rol=rol_author))
if not eitem_sh['author_org_name']:
eitem_sh['author_org_name'] = SH_UNKNOWN_VALUE
if not eitem_sh['author_name']:
eitem_sh['author_name'] = SH_UNKNOWN_VALUE
if not eitem_sh['author_user_name']:
eitem_sh['author_user_name'] = SH_UNKNOWN_VALUE
return eitem_sh | [
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19,726 | chaoss/grimoirelab-elk | grimoire_elk/enriched/enrich.py | Enrich.get_sh_ids | def get_sh_ids(self, identity, backend_name):
""" Return the Sorting Hat id and uuid for an identity """
# Convert the dict to tuple so it is hashable
identity_tuple = tuple(identity.items())
sh_ids = self.__get_sh_ids_cache(identity_tuple, backend_name)
return sh_ids | python | def get_sh_ids(self, identity, backend_name):
# Convert the dict to tuple so it is hashable
identity_tuple = tuple(identity.items())
sh_ids = self.__get_sh_ids_cache(identity_tuple, backend_name)
return sh_ids | [
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19,727 | chaoss/grimoirelab-elk | grimoire_elk/elastic_items.py | ElasticItems.get_repository_filter_raw | def get_repository_filter_raw(self, term=False):
""" Returns the filter to be used in queries in a repository items """
perceval_backend_name = self.get_connector_name()
filter_ = get_repository_filter(self.perceval_backend, perceval_backend_name, term)
return filter_ | python | def get_repository_filter_raw(self, term=False):
perceval_backend_name = self.get_connector_name()
filter_ = get_repository_filter(self.perceval_backend, perceval_backend_name, term)
return filter_ | [
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19,728 | chaoss/grimoirelab-elk | grimoire_elk/elastic_items.py | ElasticItems.set_filter_raw | def set_filter_raw(self, filter_raw):
"""Filter to be used when getting items from Ocean index"""
self.filter_raw = filter_raw
self.filter_raw_dict = []
splitted = re.compile(FILTER_SEPARATOR).split(filter_raw)
for fltr_raw in splitted:
fltr = self.__process_filter(fltr_raw)
self.filter_raw_dict.append(fltr) | python | def set_filter_raw(self, filter_raw):
self.filter_raw = filter_raw
self.filter_raw_dict = []
splitted = re.compile(FILTER_SEPARATOR).split(filter_raw)
for fltr_raw in splitted:
fltr = self.__process_filter(fltr_raw)
self.filter_raw_dict.append(fltr) | [
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19,729 | chaoss/grimoirelab-elk | grimoire_elk/elastic_items.py | ElasticItems.set_filter_raw_should | def set_filter_raw_should(self, filter_raw_should):
"""Bool filter should to be used when getting items from Ocean index"""
self.filter_raw_should = filter_raw_should
self.filter_raw_should_dict = []
splitted = re.compile(FILTER_SEPARATOR).split(filter_raw_should)
for fltr_raw in splitted:
fltr = self.__process_filter(fltr_raw)
self.filter_raw_should_dict.append(fltr) | python | def set_filter_raw_should(self, filter_raw_should):
self.filter_raw_should = filter_raw_should
self.filter_raw_should_dict = []
splitted = re.compile(FILTER_SEPARATOR).split(filter_raw_should)
for fltr_raw in splitted:
fltr = self.__process_filter(fltr_raw)
self.filter_raw_should_dict.append(fltr) | [
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19,730 | chaoss/grimoirelab-elk | grimoire_elk/elastic_items.py | ElasticItems.fetch | def fetch(self, _filter=None, ignore_incremental=False):
""" Fetch the items from raw or enriched index. An optional _filter
could be provided to filter the data collected """
logger.debug("Creating a elastic items generator.")
scroll_id = None
page = self.get_elastic_items(scroll_id, _filter=_filter, ignore_incremental=ignore_incremental)
if not page:
return []
scroll_id = page["_scroll_id"]
scroll_size = page['hits']['total']
if scroll_size == 0:
logger.warning("No results found from %s", self.elastic.anonymize_url(self.elastic.index_url))
return
while scroll_size > 0:
logger.debug("Fetching from %s: %d received", self.elastic.anonymize_url(self.elastic.index_url),
len(page['hits']['hits']))
for item in page['hits']['hits']:
eitem = item['_source']
yield eitem
page = self.get_elastic_items(scroll_id, _filter=_filter, ignore_incremental=ignore_incremental)
if not page:
break
scroll_size = len(page['hits']['hits'])
logger.debug("Fetching from %s: done receiving", self.elastic.anonymize_url(self.elastic.index_url)) | python | def fetch(self, _filter=None, ignore_incremental=False):
logger.debug("Creating a elastic items generator.")
scroll_id = None
page = self.get_elastic_items(scroll_id, _filter=_filter, ignore_incremental=ignore_incremental)
if not page:
return []
scroll_id = page["_scroll_id"]
scroll_size = page['hits']['total']
if scroll_size == 0:
logger.warning("No results found from %s", self.elastic.anonymize_url(self.elastic.index_url))
return
while scroll_size > 0:
logger.debug("Fetching from %s: %d received", self.elastic.anonymize_url(self.elastic.index_url),
len(page['hits']['hits']))
for item in page['hits']['hits']:
eitem = item['_source']
yield eitem
page = self.get_elastic_items(scroll_id, _filter=_filter, ignore_incremental=ignore_incremental)
if not page:
break
scroll_size = len(page['hits']['hits'])
logger.debug("Fetching from %s: done receiving", self.elastic.anonymize_url(self.elastic.index_url)) | [
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19,731 | chaoss/grimoirelab-elk | utils/index_mapping.py | find_uuid | def find_uuid(es_url, index):
""" Find the unique identifier field for a given index """
uid_field = None
# Get the first item to detect the data source and raw/enriched type
res = requests.get('%s/%s/_search?size=1' % (es_url, index))
first_item = res.json()['hits']['hits'][0]['_source']
fields = first_item.keys()
if 'uuid' in fields:
uid_field = 'uuid'
else:
# Non perceval backend
uuid_value = res.json()['hits']['hits'][0]['_id']
logging.debug("Finding unique id for %s with value %s", index, uuid_value)
for field in fields:
if first_item[field] == uuid_value:
logging.debug("Found unique id for %s: %s", index, field)
uid_field = field
break
if not uid_field:
logging.error("Can not find uid field for %s. Can not copy the index.", index)
logging.error("Try to copy it directly with elasticdump or similar.")
sys.exit(1)
return uid_field | python | def find_uuid(es_url, index):
uid_field = None
# Get the first item to detect the data source and raw/enriched type
res = requests.get('%s/%s/_search?size=1' % (es_url, index))
first_item = res.json()['hits']['hits'][0]['_source']
fields = first_item.keys()
if 'uuid' in fields:
uid_field = 'uuid'
else:
# Non perceval backend
uuid_value = res.json()['hits']['hits'][0]['_id']
logging.debug("Finding unique id for %s with value %s", index, uuid_value)
for field in fields:
if first_item[field] == uuid_value:
logging.debug("Found unique id for %s: %s", index, field)
uid_field = field
break
if not uid_field:
logging.error("Can not find uid field for %s. Can not copy the index.", index)
logging.error("Try to copy it directly with elasticdump or similar.")
sys.exit(1)
return uid_field | [
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19,732 | chaoss/grimoirelab-elk | utils/index_mapping.py | find_mapping | def find_mapping(es_url, index):
""" Find the mapping given an index """
mapping = None
backend = find_perceval_backend(es_url, index)
if backend:
mapping = backend.get_elastic_mappings()
if mapping:
logging.debug("MAPPING FOUND:\n%s", json.dumps(json.loads(mapping['items']), indent=True))
return mapping | python | def find_mapping(es_url, index):
mapping = None
backend = find_perceval_backend(es_url, index)
if backend:
mapping = backend.get_elastic_mappings()
if mapping:
logging.debug("MAPPING FOUND:\n%s", json.dumps(json.loads(mapping['items']), indent=True))
return mapping | [
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19,733 | chaoss/grimoirelab-elk | utils/index_mapping.py | get_elastic_items | def get_elastic_items(elastic, elastic_scroll_id=None, limit=None):
""" Get the items from the index """
scroll_size = limit
if not limit:
scroll_size = DEFAULT_LIMIT
if not elastic:
return None
url = elastic.index_url
max_process_items_pack_time = "5m" # 10 minutes
url += "/_search?scroll=%s&size=%i" % (max_process_items_pack_time,
scroll_size)
if elastic_scroll_id:
# Just continue with the scrolling
url = elastic.url
url += "/_search/scroll"
scroll_data = {
"scroll": max_process_items_pack_time,
"scroll_id": elastic_scroll_id
}
res = requests.post(url, data=json.dumps(scroll_data))
else:
query = """
{
"query": {
"bool": {
"must": []
}
}
}
"""
logging.debug("%s\n%s", url, json.dumps(json.loads(query), indent=4))
res = requests.post(url, data=query)
rjson = None
try:
rjson = res.json()
except Exception:
logging.error("No JSON found in %s", res.text)
logging.error("No results found from %s", url)
return rjson | python | def get_elastic_items(elastic, elastic_scroll_id=None, limit=None):
scroll_size = limit
if not limit:
scroll_size = DEFAULT_LIMIT
if not elastic:
return None
url = elastic.index_url
max_process_items_pack_time = "5m" # 10 minutes
url += "/_search?scroll=%s&size=%i" % (max_process_items_pack_time,
scroll_size)
if elastic_scroll_id:
# Just continue with the scrolling
url = elastic.url
url += "/_search/scroll"
scroll_data = {
"scroll": max_process_items_pack_time,
"scroll_id": elastic_scroll_id
}
res = requests.post(url, data=json.dumps(scroll_data))
else:
query = """
{
"query": {
"bool": {
"must": []
}
}
}
"""
logging.debug("%s\n%s", url, json.dumps(json.loads(query), indent=4))
res = requests.post(url, data=query)
rjson = None
try:
rjson = res.json()
except Exception:
logging.error("No JSON found in %s", res.text)
logging.error("No results found from %s", url)
return rjson | [
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19,734 | chaoss/grimoirelab-elk | utils/index_mapping.py | fetch | def fetch(elastic, backend, limit=None, search_after_value=None, scroll=True):
""" Fetch the items from raw or enriched index """
logging.debug("Creating a elastic items generator.")
elastic_scroll_id = None
search_after = search_after_value
while True:
if scroll:
rjson = get_elastic_items(elastic, elastic_scroll_id, limit)
else:
rjson = get_elastic_items_search(elastic, search_after, limit)
if rjson and "_scroll_id" in rjson:
elastic_scroll_id = rjson["_scroll_id"]
if rjson and "hits" in rjson:
if not rjson["hits"]["hits"]:
break
for hit in rjson["hits"]["hits"]:
item = hit['_source']
if 'sort' in hit:
search_after = hit['sort']
try:
backend._fix_item(item)
except Exception:
pass
yield item
else:
logging.error("No results found from %s", elastic.index_url)
break
return | python | def fetch(elastic, backend, limit=None, search_after_value=None, scroll=True):
logging.debug("Creating a elastic items generator.")
elastic_scroll_id = None
search_after = search_after_value
while True:
if scroll:
rjson = get_elastic_items(elastic, elastic_scroll_id, limit)
else:
rjson = get_elastic_items_search(elastic, search_after, limit)
if rjson and "_scroll_id" in rjson:
elastic_scroll_id = rjson["_scroll_id"]
if rjson and "hits" in rjson:
if not rjson["hits"]["hits"]:
break
for hit in rjson["hits"]["hits"]:
item = hit['_source']
if 'sort' in hit:
search_after = hit['sort']
try:
backend._fix_item(item)
except Exception:
pass
yield item
else:
logging.error("No results found from %s", elastic.index_url)
break
return | [
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19,735 | chaoss/grimoirelab-elk | utils/index_mapping.py | export_items | def export_items(elastic_url, in_index, out_index, elastic_url_out=None,
search_after=False, search_after_value=None, limit=None,
copy=False):
""" Export items from in_index to out_index using the correct mapping """
if not limit:
limit = DEFAULT_LIMIT
if search_after_value:
search_after_value_timestamp = int(search_after_value[0])
search_after_value_uuid = search_after_value[1]
search_after_value = [search_after_value_timestamp, search_after_value_uuid]
logging.info("Exporting items from %s/%s to %s", elastic_url, in_index, out_index)
count_res = requests.get('%s/%s/_count' % (elastic_url, in_index))
try:
count_res.raise_for_status()
except requests.exceptions.HTTPError:
if count_res.status_code == 404:
logging.error("The index does not exists: %s", in_index)
else:
logging.error(count_res.text)
sys.exit(1)
logging.info("Total items to copy: %i", count_res.json()['count'])
# Time to upload the items with the correct mapping
elastic_in = ElasticSearch(elastic_url, in_index)
if not copy:
# Create the correct mapping for the data sources detected from in_index
ds_mapping = find_mapping(elastic_url, in_index)
else:
logging.debug('Using the input index mapping')
ds_mapping = extract_mapping(elastic_url, in_index)
if not elastic_url_out:
elastic_out = ElasticSearch(elastic_url, out_index, mappings=ds_mapping)
else:
elastic_out = ElasticSearch(elastic_url_out, out_index, mappings=ds_mapping)
# Time to just copy from in_index to our_index
uid_field = find_uuid(elastic_url, in_index)
backend = find_perceval_backend(elastic_url, in_index)
if search_after:
total = elastic_out.bulk_upload(fetch(elastic_in, backend, limit,
search_after_value, scroll=False), uid_field)
else:
total = elastic_out.bulk_upload(fetch(elastic_in, backend, limit), uid_field)
logging.info("Total items copied: %i", total) | python | def export_items(elastic_url, in_index, out_index, elastic_url_out=None,
search_after=False, search_after_value=None, limit=None,
copy=False):
if not limit:
limit = DEFAULT_LIMIT
if search_after_value:
search_after_value_timestamp = int(search_after_value[0])
search_after_value_uuid = search_after_value[1]
search_after_value = [search_after_value_timestamp, search_after_value_uuid]
logging.info("Exporting items from %s/%s to %s", elastic_url, in_index, out_index)
count_res = requests.get('%s/%s/_count' % (elastic_url, in_index))
try:
count_res.raise_for_status()
except requests.exceptions.HTTPError:
if count_res.status_code == 404:
logging.error("The index does not exists: %s", in_index)
else:
logging.error(count_res.text)
sys.exit(1)
logging.info("Total items to copy: %i", count_res.json()['count'])
# Time to upload the items with the correct mapping
elastic_in = ElasticSearch(elastic_url, in_index)
if not copy:
# Create the correct mapping for the data sources detected from in_index
ds_mapping = find_mapping(elastic_url, in_index)
else:
logging.debug('Using the input index mapping')
ds_mapping = extract_mapping(elastic_url, in_index)
if not elastic_url_out:
elastic_out = ElasticSearch(elastic_url, out_index, mappings=ds_mapping)
else:
elastic_out = ElasticSearch(elastic_url_out, out_index, mappings=ds_mapping)
# Time to just copy from in_index to our_index
uid_field = find_uuid(elastic_url, in_index)
backend = find_perceval_backend(elastic_url, in_index)
if search_after:
total = elastic_out.bulk_upload(fetch(elastic_in, backend, limit,
search_after_value, scroll=False), uid_field)
else:
total = elastic_out.bulk_upload(fetch(elastic_in, backend, limit), uid_field)
logging.info("Total items copied: %i", total) | [
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19,736 | chaoss/grimoirelab-elk | grimoire_elk/enriched/gerrit.py | GerritEnrich._fix_review_dates | def _fix_review_dates(self, item):
"""Convert dates so ES detect them"""
for date_field in ['timestamp', 'createdOn', 'lastUpdated']:
if date_field in item.keys():
date_ts = item[date_field]
item[date_field] = unixtime_to_datetime(date_ts).isoformat()
if 'patchSets' in item.keys():
for patch in item['patchSets']:
pdate_ts = patch['createdOn']
patch['createdOn'] = unixtime_to_datetime(pdate_ts).isoformat()
if 'approvals' in patch:
for approval in patch['approvals']:
adate_ts = approval['grantedOn']
approval['grantedOn'] = unixtime_to_datetime(adate_ts).isoformat()
if 'comments' in item.keys():
for comment in item['comments']:
cdate_ts = comment['timestamp']
comment['timestamp'] = unixtime_to_datetime(cdate_ts).isoformat() | python | def _fix_review_dates(self, item):
for date_field in ['timestamp', 'createdOn', 'lastUpdated']:
if date_field in item.keys():
date_ts = item[date_field]
item[date_field] = unixtime_to_datetime(date_ts).isoformat()
if 'patchSets' in item.keys():
for patch in item['patchSets']:
pdate_ts = patch['createdOn']
patch['createdOn'] = unixtime_to_datetime(pdate_ts).isoformat()
if 'approvals' in patch:
for approval in patch['approvals']:
adate_ts = approval['grantedOn']
approval['grantedOn'] = unixtime_to_datetime(adate_ts).isoformat()
if 'comments' in item.keys():
for comment in item['comments']:
cdate_ts = comment['timestamp']
comment['timestamp'] = unixtime_to_datetime(cdate_ts).isoformat() | [
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19,737 | chaoss/grimoirelab-elk | grimoire_elk/enriched/bugzilla.py | BugzillaEnrich.get_sh_identity | def get_sh_identity(self, item, identity_field=None):
""" Return a Sorting Hat identity using bugzilla user data """
def fill_list_identity(identity, user_list_data):
""" Fill identity with user data in first item in list """
identity['username'] = user_list_data[0]['__text__']
if '@' in identity['username']:
identity['email'] = identity['username']
if 'name' in user_list_data[0]:
identity['name'] = user_list_data[0]['name']
return identity
identity = {}
for field in ['name', 'email', 'username']:
# Basic fields in Sorting Hat
identity[field] = None
user = item # by default a specific user dict is used
if 'data' in item and type(item) == dict:
user = item['data'][identity_field]
identity = fill_list_identity(identity, user)
return identity | python | def get_sh_identity(self, item, identity_field=None):
def fill_list_identity(identity, user_list_data):
""" Fill identity with user data in first item in list """
identity['username'] = user_list_data[0]['__text__']
if '@' in identity['username']:
identity['email'] = identity['username']
if 'name' in user_list_data[0]:
identity['name'] = user_list_data[0]['name']
return identity
identity = {}
for field in ['name', 'email', 'username']:
# Basic fields in Sorting Hat
identity[field] = None
user = item # by default a specific user dict is used
if 'data' in item and type(item) == dict:
user = item['data'][identity_field]
identity = fill_list_identity(identity, user)
return identity | [
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19,738 | chaoss/grimoirelab-elk | grimoire_elk/enriched/ceres_base.py | CeresBase.analyze | def analyze(self):
"""Populate an enriched index by processing input items in blocks.
:return: total number of out_items written.
"""
from_date = self._out.latest_date()
if from_date:
logger.info("Reading items since " + from_date)
else:
logger.info("Reading items since the beginning of times")
cont = 0
total_processed = 0
total_written = 0
for item_block in self._in.read_block(size=self._block_size, from_date=from_date):
cont = cont + len(item_block)
process_results = self.process(item_block)
total_processed += process_results.processed
if len(process_results.out_items) > 0:
self._out.write(process_results.out_items)
total_written += len(process_results.out_items)
else:
logger.info("No new items to be written this time.")
logger.info(
"Items read/to be written/total read/total processed/total written: "
"{0}/{1}/{2}/{3}/{4}".format(str(len(item_block)),
str(len(process_results.out_items)),
str(cont),
str(total_processed),
str(total_written)))
logger.info("SUMMARY: Items total read/total processed/total written: "
"{0}/{1}/{2}".format(str(cont),
str(total_processed),
str(total_written)))
logger.info("This is the end.")
return total_written | python | def analyze(self):
from_date = self._out.latest_date()
if from_date:
logger.info("Reading items since " + from_date)
else:
logger.info("Reading items since the beginning of times")
cont = 0
total_processed = 0
total_written = 0
for item_block in self._in.read_block(size=self._block_size, from_date=from_date):
cont = cont + len(item_block)
process_results = self.process(item_block)
total_processed += process_results.processed
if len(process_results.out_items) > 0:
self._out.write(process_results.out_items)
total_written += len(process_results.out_items)
else:
logger.info("No new items to be written this time.")
logger.info(
"Items read/to be written/total read/total processed/total written: "
"{0}/{1}/{2}/{3}/{4}".format(str(len(item_block)),
str(len(process_results.out_items)),
str(cont),
str(total_processed),
str(total_written)))
logger.info("SUMMARY: Items total read/total processed/total written: "
"{0}/{1}/{2}".format(str(cont),
str(total_processed),
str(total_written)))
logger.info("This is the end.")
return total_written | [
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19,739 | chaoss/grimoirelab-elk | grimoire_elk/enriched/ceres_base.py | ESConnector.read_item | def read_item(self, from_date=None):
"""Read items and return them one by one.
:param from_date: start date for incremental reading.
:return: next single item when any available.
:raises ValueError: `metadata__timestamp` field not found in index
:raises NotFoundError: index not found in ElasticSearch
"""
search_query = self._build_search_query(from_date)
for hit in helpers.scan(self._es_conn,
search_query,
scroll='300m',
index=self._es_index,
preserve_order=True):
yield hit | python | def read_item(self, from_date=None):
search_query = self._build_search_query(from_date)
for hit in helpers.scan(self._es_conn,
search_query,
scroll='300m',
index=self._es_index,
preserve_order=True):
yield hit | [
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19,740 | chaoss/grimoirelab-elk | grimoire_elk/enriched/ceres_base.py | ESConnector.read_block | def read_block(self, size, from_date=None):
"""Read items and return them in blocks.
:param from_date: start date for incremental reading.
:param size: block size.
:return: next block of items when any available.
:raises ValueError: `metadata__timestamp` field not found in index
:raises NotFoundError: index not found in ElasticSearch
"""
search_query = self._build_search_query(from_date)
hits_block = []
for hit in helpers.scan(self._es_conn,
search_query,
scroll='300m',
index=self._es_index,
preserve_order=True):
hits_block.append(hit)
if len(hits_block) % size == 0:
yield hits_block
# Reset hits block
hits_block = []
if len(hits_block) > 0:
yield hits_block | python | def read_block(self, size, from_date=None):
search_query = self._build_search_query(from_date)
hits_block = []
for hit in helpers.scan(self._es_conn,
search_query,
scroll='300m',
index=self._es_index,
preserve_order=True):
hits_block.append(hit)
if len(hits_block) % size == 0:
yield hits_block
# Reset hits block
hits_block = []
if len(hits_block) > 0:
yield hits_block | [
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19,741 | chaoss/grimoirelab-elk | grimoire_elk/enriched/ceres_base.py | ESConnector.write | def write(self, items):
"""Upload items to ElasticSearch.
:param items: items to be uploaded.
"""
if self._read_only:
raise IOError("Cannot write, Connector created as Read Only")
# Uploading info to the new ES
docs = []
for item in items:
doc = {
"_index": self._es_index,
"_type": "item",
"_id": item["_id"],
"_source": item["_source"]
}
docs.append(doc)
# TODO exception and error handling
helpers.bulk(self._es_conn, docs)
logger.info(self.__log_prefix + " Written: " + str(len(docs))) | python | def write(self, items):
if self._read_only:
raise IOError("Cannot write, Connector created as Read Only")
# Uploading info to the new ES
docs = []
for item in items:
doc = {
"_index": self._es_index,
"_type": "item",
"_id": item["_id"],
"_source": item["_source"]
}
docs.append(doc)
# TODO exception and error handling
helpers.bulk(self._es_conn, docs)
logger.info(self.__log_prefix + " Written: " + str(len(docs))) | [
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19,742 | chaoss/grimoirelab-elk | grimoire_elk/enriched/ceres_base.py | ESConnector.create_alias | def create_alias(self, alias_name):
"""Creates an alias pointing to the index configured in this connection"""
return self._es_conn.indices.put_alias(index=self._es_index, name=alias_name) | python | def create_alias(self, alias_name):
return self._es_conn.indices.put_alias(index=self._es_index, name=alias_name) | [
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19,743 | chaoss/grimoirelab-elk | grimoire_elk/enriched/ceres_base.py | ESConnector.exists_alias | def exists_alias(self, alias_name, index_name=None):
"""Check whether or not the given alias exists
:return: True if alias already exist"""
return self._es_conn.indices.exists_alias(index=index_name, name=alias_name) | python | def exists_alias(self, alias_name, index_name=None):
return self._es_conn.indices.exists_alias(index=index_name, name=alias_name) | [
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19,744 | chaoss/grimoirelab-elk | grimoire_elk/enriched/ceres_base.py | ESConnector._build_search_query | def _build_search_query(self, from_date):
"""Build an ElasticSearch search query to retrieve items for read methods.
:param from_date: date to start retrieving items from.
:return: JSON query in dict format
"""
sort = [{self._sort_on_field: {"order": "asc"}}]
filters = []
if self._repo:
filters.append({"term": {"origin": self._repo}})
if from_date:
filters.append({"range": {self._sort_on_field: {"gte": from_date}}})
if filters:
query = {"bool": {"filter": filters}}
else:
query = {"match_all": {}}
search_query = {
"query": query,
"sort": sort
}
return search_query | python | def _build_search_query(self, from_date):
sort = [{self._sort_on_field: {"order": "asc"}}]
filters = []
if self._repo:
filters.append({"term": {"origin": self._repo}})
if from_date:
filters.append({"range": {self._sort_on_field: {"gte": from_date}}})
if filters:
query = {"bool": {"filter": filters}}
else:
query = {"match_all": {}}
search_query = {
"query": query,
"sort": sort
}
return search_query | [
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19,745 | chaoss/grimoirelab-elk | grimoire_elk/raw/elastic.py | ElasticOcean.add_params | def add_params(cls, cmdline_parser):
""" Shared params in all backends """
parser = cmdline_parser
parser.add_argument("-e", "--elastic_url", default="http://127.0.0.1:9200",
help="Host with elastic search (default: http://127.0.0.1:9200)")
parser.add_argument("--elastic_url-enrich",
help="Host with elastic search and enriched indexes") | python | def add_params(cls, cmdline_parser):
parser = cmdline_parser
parser.add_argument("-e", "--elastic_url", default="http://127.0.0.1:9200",
help="Host with elastic search (default: http://127.0.0.1:9200)")
parser.add_argument("--elastic_url-enrich",
help="Host with elastic search and enriched indexes") | [
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19,746 | chaoss/grimoirelab-elk | grimoire_elk/raw/elastic.py | ElasticOcean.get_p2o_params_from_url | def get_p2o_params_from_url(cls, url):
""" Get the p2o params given a URL for the data source """
# if the url doesn't contain a filter separator, return it
if PRJ_JSON_FILTER_SEPARATOR not in url:
return {"url": url}
# otherwise, add the url to the params
params = {'url': url.split(' ', 1)[0]}
# tokenize the filter and add them to the param dict
tokens = url.split(PRJ_JSON_FILTER_SEPARATOR)[1:]
if len(tokens) > 1:
cause = "Too many filters defined for %s, only the first one is considered" % url
logger.warning(cause)
token = tokens[0]
filter_tokens = token.split(PRJ_JSON_FILTER_OP_ASSIGNMENT)
if len(filter_tokens) != 2:
cause = "Too many tokens after splitting for %s in %s" % (token, url)
logger.error(cause)
raise ELKError(cause=cause)
fltr_name = filter_tokens[0].strip()
fltr_value = filter_tokens[1].strip()
params['filter-' + fltr_name] = fltr_value
return params | python | def get_p2o_params_from_url(cls, url):
# if the url doesn't contain a filter separator, return it
if PRJ_JSON_FILTER_SEPARATOR not in url:
return {"url": url}
# otherwise, add the url to the params
params = {'url': url.split(' ', 1)[0]}
# tokenize the filter and add them to the param dict
tokens = url.split(PRJ_JSON_FILTER_SEPARATOR)[1:]
if len(tokens) > 1:
cause = "Too many filters defined for %s, only the first one is considered" % url
logger.warning(cause)
token = tokens[0]
filter_tokens = token.split(PRJ_JSON_FILTER_OP_ASSIGNMENT)
if len(filter_tokens) != 2:
cause = "Too many tokens after splitting for %s in %s" % (token, url)
logger.error(cause)
raise ELKError(cause=cause)
fltr_name = filter_tokens[0].strip()
fltr_value = filter_tokens[1].strip()
params['filter-' + fltr_name] = fltr_value
return params | [
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19,747 | chaoss/grimoirelab-elk | grimoire_elk/raw/elastic.py | ElasticOcean.feed | def feed(self, from_date=None, from_offset=None, category=None,
latest_items=None, arthur_items=None, filter_classified=None):
""" Feed data in Elastic from Perceval or Arthur """
if self.fetch_archive:
items = self.perceval_backend.fetch_from_archive()
self.feed_items(items)
return
elif arthur_items:
items = arthur_items
self.feed_items(items)
return
if from_date and from_offset:
raise RuntimeError("Can't not feed using from_date and from_offset.")
# We need to filter by repository to support several repositories
# in the same raw index
filters_ = [get_repository_filter(self.perceval_backend,
self.get_connector_name())]
# Check if backend supports from_date
signature = inspect.signature(self.perceval_backend.fetch)
last_update = None
if 'from_date' in signature.parameters:
if from_date:
last_update = from_date
else:
self.last_update = self.get_last_update_from_es(filters_=filters_)
last_update = self.last_update
logger.info("Incremental from: %s", last_update)
offset = None
if 'offset' in signature.parameters:
if from_offset:
offset = from_offset
else:
offset = self.elastic.get_last_offset("offset", filters_=filters_)
if offset is not None:
logger.info("Incremental from: %i offset", offset)
else:
logger.info("Not incremental")
params = {}
# category and filter_classified params are shared
# by all Perceval backends
if category is not None:
params['category'] = category
if filter_classified is not None:
params['filter_classified'] = filter_classified
# latest items, from_date and offset cannot be used together,
# thus, the params dictionary is filled with the param available
# and Perceval is executed
if latest_items:
params['latest_items'] = latest_items
items = self.perceval_backend.fetch(**params)
elif last_update:
last_update = last_update.replace(tzinfo=None)
params['from_date'] = last_update
items = self.perceval_backend.fetch(**params)
elif offset is not None:
params['offset'] = offset
items = self.perceval_backend.fetch(**params)
else:
items = self.perceval_backend.fetch(**params)
self.feed_items(items)
self.update_items() | python | def feed(self, from_date=None, from_offset=None, category=None,
latest_items=None, arthur_items=None, filter_classified=None):
if self.fetch_archive:
items = self.perceval_backend.fetch_from_archive()
self.feed_items(items)
return
elif arthur_items:
items = arthur_items
self.feed_items(items)
return
if from_date and from_offset:
raise RuntimeError("Can't not feed using from_date and from_offset.")
# We need to filter by repository to support several repositories
# in the same raw index
filters_ = [get_repository_filter(self.perceval_backend,
self.get_connector_name())]
# Check if backend supports from_date
signature = inspect.signature(self.perceval_backend.fetch)
last_update = None
if 'from_date' in signature.parameters:
if from_date:
last_update = from_date
else:
self.last_update = self.get_last_update_from_es(filters_=filters_)
last_update = self.last_update
logger.info("Incremental from: %s", last_update)
offset = None
if 'offset' in signature.parameters:
if from_offset:
offset = from_offset
else:
offset = self.elastic.get_last_offset("offset", filters_=filters_)
if offset is not None:
logger.info("Incremental from: %i offset", offset)
else:
logger.info("Not incremental")
params = {}
# category and filter_classified params are shared
# by all Perceval backends
if category is not None:
params['category'] = category
if filter_classified is not None:
params['filter_classified'] = filter_classified
# latest items, from_date and offset cannot be used together,
# thus, the params dictionary is filled with the param available
# and Perceval is executed
if latest_items:
params['latest_items'] = latest_items
items = self.perceval_backend.fetch(**params)
elif last_update:
last_update = last_update.replace(tzinfo=None)
params['from_date'] = last_update
items = self.perceval_backend.fetch(**params)
elif offset is not None:
params['offset'] = offset
items = self.perceval_backend.fetch(**params)
else:
items = self.perceval_backend.fetch(**params)
self.feed_items(items)
self.update_items() | [
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19,748 | chaoss/grimoirelab-elk | grimoire_elk/enriched/git.py | GitEnrich.get_identities | def get_identities(self, item):
""" Return the identities from an item.
If the repo is in GitHub, get the usernames from GitHub. """
def add_sh_github_identity(user, user_field, rol):
""" Add a new github identity to SH if it does not exists """
github_repo = None
if GITHUB in item['origin']:
github_repo = item['origin'].replace(GITHUB, '')
github_repo = re.sub('.git$', '', github_repo)
if not github_repo:
return
# Try to get the identity from SH
user_data = item['data'][user_field]
sh_identity = SortingHat.get_github_commit_username(self.sh_db, user, SH_GIT_COMMIT)
if not sh_identity:
# Get the usename from GitHub
gh_username = self.get_github_login(user_data, rol, commit_hash, github_repo)
# Create a new SH identity with name, email from git and username from github
logger.debug("Adding new identity %s to SH %s: %s", gh_username, SH_GIT_COMMIT, user)
user = self.get_sh_identity(user_data)
user['username'] = gh_username
SortingHat.add_identity(self.sh_db, user, SH_GIT_COMMIT)
else:
if user_data not in self.github_logins:
self.github_logins[user_data] = sh_identity['username']
logger.debug("GitHub-commit exists. username:%s user:%s",
sh_identity['username'], user_data)
commit_hash = item['data']['commit']
if item['data']['Author']:
# Check multi authors commits
m = self.AUTHOR_P2P_REGEX.match(item['data']["Author"])
n = self.AUTHOR_P2P_NEW_REGEX.match(item['data']["Author"])
if (m or n) and self.pair_programming:
authors = self.__get_authors(item['data']["Author"])
for author in authors:
user = self.get_sh_identity(author)
yield user
else:
user = self.get_sh_identity(item['data']["Author"])
yield user
if self.github_token:
add_sh_github_identity(user, 'Author', 'author')
if item['data']['Commit']:
m = self.AUTHOR_P2P_REGEX.match(item['data']["Commit"])
n = self.AUTHOR_P2P_NEW_REGEX.match(item['data']["Author"])
if (m or n) and self.pair_programming:
committers = self.__get_authors(item['data']['Commit'])
for committer in committers:
user = self.get_sh_identity(committer)
yield user
else:
user = self.get_sh_identity(item['data']['Commit'])
yield user
if self.github_token:
add_sh_github_identity(user, 'Commit', 'committer')
if 'Signed-off-by' in item['data'] and self.pair_programming:
signers = item['data']["Signed-off-by"]
for signer in signers:
user = self.get_sh_identity(signer)
yield user | python | def get_identities(self, item):
def add_sh_github_identity(user, user_field, rol):
""" Add a new github identity to SH if it does not exists """
github_repo = None
if GITHUB in item['origin']:
github_repo = item['origin'].replace(GITHUB, '')
github_repo = re.sub('.git$', '', github_repo)
if not github_repo:
return
# Try to get the identity from SH
user_data = item['data'][user_field]
sh_identity = SortingHat.get_github_commit_username(self.sh_db, user, SH_GIT_COMMIT)
if not sh_identity:
# Get the usename from GitHub
gh_username = self.get_github_login(user_data, rol, commit_hash, github_repo)
# Create a new SH identity with name, email from git and username from github
logger.debug("Adding new identity %s to SH %s: %s", gh_username, SH_GIT_COMMIT, user)
user = self.get_sh_identity(user_data)
user['username'] = gh_username
SortingHat.add_identity(self.sh_db, user, SH_GIT_COMMIT)
else:
if user_data not in self.github_logins:
self.github_logins[user_data] = sh_identity['username']
logger.debug("GitHub-commit exists. username:%s user:%s",
sh_identity['username'], user_data)
commit_hash = item['data']['commit']
if item['data']['Author']:
# Check multi authors commits
m = self.AUTHOR_P2P_REGEX.match(item['data']["Author"])
n = self.AUTHOR_P2P_NEW_REGEX.match(item['data']["Author"])
if (m or n) and self.pair_programming:
authors = self.__get_authors(item['data']["Author"])
for author in authors:
user = self.get_sh_identity(author)
yield user
else:
user = self.get_sh_identity(item['data']["Author"])
yield user
if self.github_token:
add_sh_github_identity(user, 'Author', 'author')
if item['data']['Commit']:
m = self.AUTHOR_P2P_REGEX.match(item['data']["Commit"])
n = self.AUTHOR_P2P_NEW_REGEX.match(item['data']["Author"])
if (m or n) and self.pair_programming:
committers = self.__get_authors(item['data']['Commit'])
for committer in committers:
user = self.get_sh_identity(committer)
yield user
else:
user = self.get_sh_identity(item['data']['Commit'])
yield user
if self.github_token:
add_sh_github_identity(user, 'Commit', 'committer')
if 'Signed-off-by' in item['data'] and self.pair_programming:
signers = item['data']["Signed-off-by"]
for signer in signers:
user = self.get_sh_identity(signer)
yield user | [
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19,749 | chaoss/grimoirelab-elk | grimoire_elk/enriched/git.py | GitEnrich.__fix_field_date | def __fix_field_date(self, item, attribute):
"""Fix possible errors in the field date"""
field_date = str_to_datetime(item[attribute])
try:
_ = int(field_date.strftime("%z")[0:3])
except ValueError:
logger.warning("%s in commit %s has a wrong format", attribute, item['commit'])
item[attribute] = field_date.replace(tzinfo=None).isoformat() | python | def __fix_field_date(self, item, attribute):
field_date = str_to_datetime(item[attribute])
try:
_ = int(field_date.strftime("%z")[0:3])
except ValueError:
logger.warning("%s in commit %s has a wrong format", attribute, item['commit'])
item[attribute] = field_date.replace(tzinfo=None).isoformat() | [
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19,750 | chaoss/grimoirelab-elk | grimoire_elk/enriched/git.py | GitEnrich.update_items | def update_items(self, ocean_backend, enrich_backend):
"""Retrieve the commits not present in the original repository and delete
the corresponding documents from the raw and enriched indexes"""
fltr = {
'name': 'origin',
'value': [self.perceval_backend.origin]
}
logger.debug("[update-items] Checking commits for %s.", self.perceval_backend.origin)
git_repo = GitRepository(self.perceval_backend.uri, self.perceval_backend.gitpath)
try:
current_hashes = set([commit for commit in git_repo.rev_list()])
except Exception as e:
logger.error("Skip updating branch info for repo %s, git rev-list command failed: %s", git_repo.uri, e)
return
raw_hashes = set([item['data']['commit']
for item in ocean_backend.fetch(ignore_incremental=True, _filter=fltr)])
hashes_to_delete = list(raw_hashes.difference(current_hashes))
to_process = []
for _hash in hashes_to_delete:
to_process.append(_hash)
if len(to_process) != MAX_BULK_UPDATE_SIZE:
continue
# delete documents from the raw index
self.remove_commits(to_process, ocean_backend.elastic.index_url,
'data.commit', self.perceval_backend.origin)
# delete documents from the enriched index
self.remove_commits(to_process, enrich_backend.elastic.index_url,
'hash', self.perceval_backend.origin)
to_process = []
if to_process:
# delete documents from the raw index
self.remove_commits(to_process, ocean_backend.elastic.index_url,
'data.commit', self.perceval_backend.origin)
# delete documents from the enriched index
self.remove_commits(to_process, enrich_backend.elastic.index_url,
'hash', self.perceval_backend.origin)
logger.debug("[update-items] %s commits deleted from %s with origin %s.",
len(hashes_to_delete), ocean_backend.elastic.anonymize_url(ocean_backend.elastic.index_url),
self.perceval_backend.origin)
logger.debug("[update-items] %s commits deleted from %s with origin %s.",
len(hashes_to_delete), enrich_backend.elastic.anonymize_url(enrich_backend.elastic.index_url),
self.perceval_backend.origin)
# update branch info
self.delete_commit_branches(enrich_backend)
self.add_commit_branches(git_repo, enrich_backend) | python | def update_items(self, ocean_backend, enrich_backend):
fltr = {
'name': 'origin',
'value': [self.perceval_backend.origin]
}
logger.debug("[update-items] Checking commits for %s.", self.perceval_backend.origin)
git_repo = GitRepository(self.perceval_backend.uri, self.perceval_backend.gitpath)
try:
current_hashes = set([commit for commit in git_repo.rev_list()])
except Exception as e:
logger.error("Skip updating branch info for repo %s, git rev-list command failed: %s", git_repo.uri, e)
return
raw_hashes = set([item['data']['commit']
for item in ocean_backend.fetch(ignore_incremental=True, _filter=fltr)])
hashes_to_delete = list(raw_hashes.difference(current_hashes))
to_process = []
for _hash in hashes_to_delete:
to_process.append(_hash)
if len(to_process) != MAX_BULK_UPDATE_SIZE:
continue
# delete documents from the raw index
self.remove_commits(to_process, ocean_backend.elastic.index_url,
'data.commit', self.perceval_backend.origin)
# delete documents from the enriched index
self.remove_commits(to_process, enrich_backend.elastic.index_url,
'hash', self.perceval_backend.origin)
to_process = []
if to_process:
# delete documents from the raw index
self.remove_commits(to_process, ocean_backend.elastic.index_url,
'data.commit', self.perceval_backend.origin)
# delete documents from the enriched index
self.remove_commits(to_process, enrich_backend.elastic.index_url,
'hash', self.perceval_backend.origin)
logger.debug("[update-items] %s commits deleted from %s with origin %s.",
len(hashes_to_delete), ocean_backend.elastic.anonymize_url(ocean_backend.elastic.index_url),
self.perceval_backend.origin)
logger.debug("[update-items] %s commits deleted from %s with origin %s.",
len(hashes_to_delete), enrich_backend.elastic.anonymize_url(enrich_backend.elastic.index_url),
self.perceval_backend.origin)
# update branch info
self.delete_commit_branches(enrich_backend)
self.add_commit_branches(git_repo, enrich_backend) | [
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19,751 | chaoss/grimoirelab-elk | grimoire_elk/enriched/git.py | GitEnrich.add_commit_branches | def add_commit_branches(self, git_repo, enrich_backend):
"""Add the information about branches to the documents representing commits in
the enriched index. Branches are obtained using the command `git ls-remote`,
then for each branch, the list of commits is retrieved via the command `git rev-list branch-name` and
used to update the corresponding items in the enriched index.
:param git_repo: GitRepository object
:param enrich_backend: the enrich backend
"""
to_process = []
for hash, refname in git_repo._discover_refs(remote=True):
if not refname.startswith('refs/heads/'):
continue
commit_count = 0
branch_name = refname.replace('refs/heads/', '')
try:
commits = git_repo.rev_list([branch_name])
for commit in commits:
to_process.append(commit)
commit_count += 1
if commit_count == MAX_BULK_UPDATE_SIZE:
self.__process_commits_in_branch(enrich_backend, branch_name, to_process)
# reset the counter
to_process = []
commit_count = 0
if commit_count:
self.__process_commits_in_branch(enrich_backend, branch_name, to_process)
except Exception as e:
logger.error("Skip adding branch info for repo %s due to %s", git_repo.uri, e)
return | python | def add_commit_branches(self, git_repo, enrich_backend):
to_process = []
for hash, refname in git_repo._discover_refs(remote=True):
if not refname.startswith('refs/heads/'):
continue
commit_count = 0
branch_name = refname.replace('refs/heads/', '')
try:
commits = git_repo.rev_list([branch_name])
for commit in commits:
to_process.append(commit)
commit_count += 1
if commit_count == MAX_BULK_UPDATE_SIZE:
self.__process_commits_in_branch(enrich_backend, branch_name, to_process)
# reset the counter
to_process = []
commit_count = 0
if commit_count:
self.__process_commits_in_branch(enrich_backend, branch_name, to_process)
except Exception as e:
logger.error("Skip adding branch info for repo %s due to %s", git_repo.uri, e)
return | [
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19,752 | chaoss/grimoirelab-elk | utils/gelk_mapping.py | find_ds_mapping | def find_ds_mapping(data_source, es_major_version):
"""
Find the mapping given a perceval data source
:param data_source: name of the perceval data source
:param es_major_version: string with the major version for Elasticsearch
:return: a dict with the mappings (raw and enriched)
"""
mappings = {"raw": None,
"enriched": None}
# Backend connectors
connectors = get_connectors()
try:
raw_klass = connectors[data_source][1]
enrich_klass = connectors[data_source][2]
except KeyError:
print("Data source not found", data_source)
sys.exit(1)
# Mapping for raw index
backend = raw_klass(None)
if backend:
mapping = json.loads(backend.mapping.get_elastic_mappings(es_major_version)['items'])
mappings['raw'] = [mapping, find_general_mappings(es_major_version)]
# Mapping for enriched index
backend = enrich_klass(None)
if backend:
mapping = json.loads(backend.mapping.get_elastic_mappings(es_major_version)['items'])
mappings['enriched'] = [mapping, find_general_mappings(es_major_version)]
return mappings | python | def find_ds_mapping(data_source, es_major_version):
mappings = {"raw": None,
"enriched": None}
# Backend connectors
connectors = get_connectors()
try:
raw_klass = connectors[data_source][1]
enrich_klass = connectors[data_source][2]
except KeyError:
print("Data source not found", data_source)
sys.exit(1)
# Mapping for raw index
backend = raw_klass(None)
if backend:
mapping = json.loads(backend.mapping.get_elastic_mappings(es_major_version)['items'])
mappings['raw'] = [mapping, find_general_mappings(es_major_version)]
# Mapping for enriched index
backend = enrich_klass(None)
if backend:
mapping = json.loads(backend.mapping.get_elastic_mappings(es_major_version)['items'])
mappings['enriched'] = [mapping, find_general_mappings(es_major_version)]
return mappings | [
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19,753 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_aoc.py | areas_of_code | def areas_of_code(git_enrich, in_conn, out_conn, block_size=100):
"""Build and index for areas of code from a given Perceval RAW index.
:param block_size: size of items block.
:param git_enrich: GitEnrich object to deal with SortingHat affiliations.
:param in_conn: ESPandasConnector to read from.
:param out_conn: ESPandasConnector to write to.
:return: number of documents written in ElasticSearch enriched index.
"""
aoc = AreasOfCode(in_connector=in_conn, out_connector=out_conn, block_size=block_size,
git_enrich=git_enrich)
ndocs = aoc.analyze()
return ndocs | python | def areas_of_code(git_enrich, in_conn, out_conn, block_size=100):
aoc = AreasOfCode(in_connector=in_conn, out_connector=out_conn, block_size=block_size,
git_enrich=git_enrich)
ndocs = aoc.analyze()
return ndocs | [
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... | Build and index for areas of code from a given Perceval RAW index.
:param block_size: size of items block.
:param git_enrich: GitEnrich object to deal with SortingHat affiliations.
:param in_conn: ESPandasConnector to read from.
:param out_conn: ESPandasConnector to write to.
:return: number of documents written in ElasticSearch enriched index. | [
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19,754 | chaoss/grimoirelab-elk | grimoire_elk/enriched/study_ceres_aoc.py | AreasOfCode.process | def process(self, items_block):
"""Process items to add file related information.
Eventize items creating one new item per each file found in the commit (excluding
files with no actions performed on them). For each event, file path, file name,
path parts, file type and file extension are added as fields.
:param items_block: items to be processed. Expects to find ElasticSearch hits _source part only.
"""
logger.info(self.__log_prefix + " New commits: " + str(len(items_block)))
# Create events from commits
git_events = Git(items_block, self._git_enrich)
events_df = git_events.eventize(2)
logger.info(self.__log_prefix + " New events: " + str(len(events_df)))
if len(events_df) > 0:
# Filter information
data_filtered = FilterRows(events_df)
events_df = data_filtered.filter_(["filepath"], "-")
logger.info(self.__log_prefix + " New events filtered: " + str(len(events_df)))
events_df['message'] = events_df['message'].str.slice(stop=AreasOfCode.MESSAGE_MAX_SIZE)
logger.info(self.__log_prefix + " Remove message content")
# Add filetype info
enriched_filetype = FileType(events_df)
events_df = enriched_filetype.enrich('filepath')
logger.info(self.__log_prefix + " New Filetype events: " + str(len(events_df)))
# Split filepath info
enriched_filepath = FilePath(events_df)
events_df = enriched_filepath.enrich('filepath')
logger.info(self.__log_prefix + " New Filepath events: " + str(len(events_df)))
# Deal with surrogates
convert = ToUTF8(events_df)
events_df = convert.enrich(["owner"])
logger.info(self.__log_prefix + " Final new events: " + str(len(events_df)))
return self.ProcessResults(processed=len(events_df), out_items=events_df) | python | def process(self, items_block):
logger.info(self.__log_prefix + " New commits: " + str(len(items_block)))
# Create events from commits
git_events = Git(items_block, self._git_enrich)
events_df = git_events.eventize(2)
logger.info(self.__log_prefix + " New events: " + str(len(events_df)))
if len(events_df) > 0:
# Filter information
data_filtered = FilterRows(events_df)
events_df = data_filtered.filter_(["filepath"], "-")
logger.info(self.__log_prefix + " New events filtered: " + str(len(events_df)))
events_df['message'] = events_df['message'].str.slice(stop=AreasOfCode.MESSAGE_MAX_SIZE)
logger.info(self.__log_prefix + " Remove message content")
# Add filetype info
enriched_filetype = FileType(events_df)
events_df = enriched_filetype.enrich('filepath')
logger.info(self.__log_prefix + " New Filetype events: " + str(len(events_df)))
# Split filepath info
enriched_filepath = FilePath(events_df)
events_df = enriched_filepath.enrich('filepath')
logger.info(self.__log_prefix + " New Filepath events: " + str(len(events_df)))
# Deal with surrogates
convert = ToUTF8(events_df)
events_df = convert.enrich(["owner"])
logger.info(self.__log_prefix + " Final new events: " + str(len(events_df)))
return self.ProcessResults(processed=len(events_df), out_items=events_df) | [
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19,755 | chaoss/grimoirelab-elk | grimoire_elk/enriched/utils.py | get_time_diff_days | def get_time_diff_days(start, end):
''' Number of days between two dates in UTC format '''
if start is None or end is None:
return None
if type(start) is not datetime.datetime:
start = parser.parse(start).replace(tzinfo=None)
if type(end) is not datetime.datetime:
end = parser.parse(end).replace(tzinfo=None)
seconds_day = float(60 * 60 * 24)
diff_days = (end - start).total_seconds() / seconds_day
diff_days = float('%.2f' % diff_days)
return diff_days | python | def get_time_diff_days(start, end):
''' Number of days between two dates in UTC format '''
if start is None or end is None:
return None
if type(start) is not datetime.datetime:
start = parser.parse(start).replace(tzinfo=None)
if type(end) is not datetime.datetime:
end = parser.parse(end).replace(tzinfo=None)
seconds_day = float(60 * 60 * 24)
diff_days = (end - start).total_seconds() / seconds_day
diff_days = float('%.2f' % diff_days)
return diff_days | [
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19,756 | chaoss/grimoirelab-elk | grimoire_elk/enriched/phabricator.py | PhabricatorEnrich.__fill_phab_ids | def __fill_phab_ids(self, item):
""" Get mappings between phab ids and names """
for p in item['projects']:
if p and 'name' in p and 'phid' in p:
self.phab_ids_names[p['phid']] = p['name']
if 'authorData' not in item['fields'] or not item['fields']['authorData']:
return
self.phab_ids_names[item['fields']['authorData']['phid']] = item['fields']['authorData']['userName']
if 'ownerData' in item['fields'] and item['fields']['ownerData']:
self.phab_ids_names[item['fields']['ownerData']['phid']] = item['fields']['ownerData']['userName']
if 'priority' in item['fields']:
val = item['fields']['priority']['value']
self.phab_ids_names[str(val)] = item['fields']['priority']['name']
for t in item['transactions']:
if 'authorData' in t and t['authorData'] and 'userName' in t['authorData']:
self.phab_ids_names[t['authorData']['phid']] = t['authorData']['userName']
elif t['authorData'] and 'name' in t['authorData']:
# Herald
self.phab_ids_names[t['authorData']['phid']] = t['authorData']['name'] | python | def __fill_phab_ids(self, item):
for p in item['projects']:
if p and 'name' in p and 'phid' in p:
self.phab_ids_names[p['phid']] = p['name']
if 'authorData' not in item['fields'] or not item['fields']['authorData']:
return
self.phab_ids_names[item['fields']['authorData']['phid']] = item['fields']['authorData']['userName']
if 'ownerData' in item['fields'] and item['fields']['ownerData']:
self.phab_ids_names[item['fields']['ownerData']['phid']] = item['fields']['ownerData']['userName']
if 'priority' in item['fields']:
val = item['fields']['priority']['value']
self.phab_ids_names[str(val)] = item['fields']['priority']['name']
for t in item['transactions']:
if 'authorData' in t and t['authorData'] and 'userName' in t['authorData']:
self.phab_ids_names[t['authorData']['phid']] = t['authorData']['userName']
elif t['authorData'] and 'name' in t['authorData']:
# Herald
self.phab_ids_names[t['authorData']['phid']] = t['authorData']['name'] | [
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19,757 | robdmc/crontabs | crontabs/crontabs.py | Tab.starting_at | def starting_at(self, datetime_or_str):
"""
Set the starting time for the cron job. If not specified, the starting time will always
be the beginning of the interval that is current when the cron is started.
:param datetime_or_str: a datetime object or a string that dateutil.parser can understand
:return: self
"""
if isinstance(datetime_or_str, str):
self._starting_at = parse(datetime_or_str)
elif isinstance(datetime_or_str, datetime.datetime):
self._starting_at = datetime_or_str
else:
raise ValueError('.starting_at() method can only take strings or datetime objects')
return self | python | def starting_at(self, datetime_or_str):
if isinstance(datetime_or_str, str):
self._starting_at = parse(datetime_or_str)
elif isinstance(datetime_or_str, datetime.datetime):
self._starting_at = datetime_or_str
else:
raise ValueError('.starting_at() method can only take strings or datetime objects')
return self | [
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19,758 | robdmc/crontabs | crontabs/crontabs.py | Tab.run | def run(self, func, *func_args, **func__kwargs):
"""
Specify the function to run at the scheduled times
:param func: a callable
:param func_args: the args to the callable
:param func__kwargs: the kwargs to the callable
:return:
"""
self._func = func
self._func_args = func_args
self._func_kwargs = func__kwargs
return self | python | def run(self, func, *func_args, **func__kwargs):
self._func = func
self._func_args = func_args
self._func_kwargs = func__kwargs
return self | [
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19,759 | robdmc/crontabs | crontabs/crontabs.py | Tab._get_target | def _get_target(self):
"""
returns a callable with no arguments designed
to be the target of a Subprocess
"""
if None in [self._func, self._func_kwargs, self._func_kwargs, self._every_kwargs]:
raise ValueError('You must call the .every() and .run() methods on every tab.')
return self._loop | python | def _get_target(self):
if None in [self._func, self._func_kwargs, self._func_kwargs, self._every_kwargs]:
raise ValueError('You must call the .every() and .run() methods on every tab.')
return self._loop | [
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19,760 | robdmc/crontabs | crontabs/processes.py | wrapped_target | def wrapped_target(target, q_stdout, q_stderr, q_error, robust, name, *args, **kwargs): # pragma: no cover
"""
Wraps a target with queues replacing stdout and stderr
"""
import sys
sys.stdout = IOQueue(q_stdout)
sys.stderr = IOQueue(q_stderr)
try:
target(*args, **kwargs)
except:
if not robust:
s = 'Error in tab\n' + traceback.format_exc()
logger = daiquiri.getLogger(name)
logger.error(s)
else:
raise
if not robust:
q_error.put(name)
raise | python | def wrapped_target(target, q_stdout, q_stderr, q_error, robust, name, *args, **kwargs): # pragma: no cover
import sys
sys.stdout = IOQueue(q_stdout)
sys.stderr = IOQueue(q_stderr)
try:
target(*args, **kwargs)
except:
if not robust:
s = 'Error in tab\n' + traceback.format_exc()
logger = daiquiri.getLogger(name)
logger.error(s)
else:
raise
if not robust:
q_error.put(name)
raise | [
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19,761 | robdmc/crontabs | crontabs/processes.py | ProcessMonitor.loop | def loop(self, max_seconds=None):
"""
Main loop for the process. This will run continuously until maxiter
"""
loop_started = datetime.datetime.now()
self._is_running = True
while self._is_running:
self.process_error_queue(self.q_error)
if max_seconds is not None:
if (datetime.datetime.now() - loop_started).total_seconds() > max_seconds:
break
for subprocess in self._subprocesses:
if not subprocess.is_alive():
subprocess.start()
self.process_io_queue(self.q_stdout, sys.stdout)
self.process_io_queue(self.q_stderr, sys.stderr) | python | def loop(self, max_seconds=None):
loop_started = datetime.datetime.now()
self._is_running = True
while self._is_running:
self.process_error_queue(self.q_error)
if max_seconds is not None:
if (datetime.datetime.now() - loop_started).total_seconds() > max_seconds:
break
for subprocess in self._subprocesses:
if not subprocess.is_alive():
subprocess.start()
self.process_io_queue(self.q_stdout, sys.stdout)
self.process_io_queue(self.q_stderr, sys.stderr) | [
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19,762 | gusutabopb/aioinflux | aioinflux/serialization/common.py | escape | def escape(string, escape_pattern):
"""Assistant function for string escaping"""
try:
return string.translate(escape_pattern)
except AttributeError:
warnings.warn("Non-string-like data passed. "
"Attempting to convert to 'str'.")
return str(string).translate(tag_escape) | python | def escape(string, escape_pattern):
try:
return string.translate(escape_pattern)
except AttributeError:
warnings.warn("Non-string-like data passed. "
"Attempting to convert to 'str'.")
return str(string).translate(tag_escape) | [
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19,763 | gusutabopb/aioinflux | aioinflux/serialization/usertype.py | _make_serializer | def _make_serializer(meas, schema, rm_none, extra_tags, placeholder): # noqa: C901
"""Factory of line protocol parsers"""
_validate_schema(schema, placeholder)
tags = []
fields = []
ts = None
meas = meas
for k, t in schema.items():
if t is MEASUREMENT:
meas = f"{{i.{k}}}"
elif t is TIMEINT:
ts = f"{{i.{k}}}"
elif t is TIMESTR:
if pd:
ts = f"{{pd.Timestamp(i.{k} or 0).value}}"
else:
ts = f"{{dt_to_int(str_to_dt(i.{k}))}}"
elif t is TIMEDT:
if pd:
ts = f"{{pd.Timestamp(i.{k} or 0).value}}"
else:
ts = f"{{dt_to_int(i.{k})}}"
elif t is TAG:
tags.append(f"{k}={{str(i.{k}).translate(tag_escape)}}")
elif t is TAGENUM:
tags.append(f"{k}={{getattr(i.{k}, 'name', i.{k} or None)}}")
elif t in (FLOAT, BOOL):
fields.append(f"{k}={{i.{k}}}")
elif t is INT:
fields.append(f"{k}={{i.{k}}}i")
elif t is STR:
fields.append(f"{k}=\\\"{{str(i.{k}).translate(str_escape)}}\\\"")
elif t is ENUM:
fields.append(f"{k}=\\\"{{getattr(i.{k}, 'name', i.{k} or None)}}\\\"")
else:
raise SchemaError(f"Invalid attribute type {k!r}: {t!r}")
extra_tags = extra_tags or {}
for k, v in extra_tags.items():
tags.append(f"{k}={v}")
if placeholder:
fields.insert(0, f"_=true")
sep = ',' if tags else ''
ts = f' {ts}' if ts else ''
fmt = f"{meas}{sep}{','.join(tags)} {','.join(fields)}{ts}"
if rm_none:
# Has substantial runtime impact. Best avoided if performance is critical.
# First field can't be removed.
pat = r',\w+="?None"?i?'
f = eval('lambda i: re.sub(r\'{}\', "", f"{}").encode()'.format(pat, fmt))
else:
f = eval('lambda i: f"{}".encode()'.format(fmt))
f.__doc__ = "Returns InfluxDB line protocol representation of user-defined class"
f._args = dict(meas=meas, schema=schema, rm_none=rm_none,
extra_tags=extra_tags, placeholder=placeholder)
return f | python | def _make_serializer(meas, schema, rm_none, extra_tags, placeholder): # noqa: C901
_validate_schema(schema, placeholder)
tags = []
fields = []
ts = None
meas = meas
for k, t in schema.items():
if t is MEASUREMENT:
meas = f"{{i.{k}}}"
elif t is TIMEINT:
ts = f"{{i.{k}}}"
elif t is TIMESTR:
if pd:
ts = f"{{pd.Timestamp(i.{k} or 0).value}}"
else:
ts = f"{{dt_to_int(str_to_dt(i.{k}))}}"
elif t is TIMEDT:
if pd:
ts = f"{{pd.Timestamp(i.{k} or 0).value}}"
else:
ts = f"{{dt_to_int(i.{k})}}"
elif t is TAG:
tags.append(f"{k}={{str(i.{k}).translate(tag_escape)}}")
elif t is TAGENUM:
tags.append(f"{k}={{getattr(i.{k}, 'name', i.{k} or None)}}")
elif t in (FLOAT, BOOL):
fields.append(f"{k}={{i.{k}}}")
elif t is INT:
fields.append(f"{k}={{i.{k}}}i")
elif t is STR:
fields.append(f"{k}=\\\"{{str(i.{k}).translate(str_escape)}}\\\"")
elif t is ENUM:
fields.append(f"{k}=\\\"{{getattr(i.{k}, 'name', i.{k} or None)}}\\\"")
else:
raise SchemaError(f"Invalid attribute type {k!r}: {t!r}")
extra_tags = extra_tags or {}
for k, v in extra_tags.items():
tags.append(f"{k}={v}")
if placeholder:
fields.insert(0, f"_=true")
sep = ',' if tags else ''
ts = f' {ts}' if ts else ''
fmt = f"{meas}{sep}{','.join(tags)} {','.join(fields)}{ts}"
if rm_none:
# Has substantial runtime impact. Best avoided if performance is critical.
# First field can't be removed.
pat = r',\w+="?None"?i?'
f = eval('lambda i: re.sub(r\'{}\', "", f"{}").encode()'.format(pat, fmt))
else:
f = eval('lambda i: f"{}".encode()'.format(fmt))
f.__doc__ = "Returns InfluxDB line protocol representation of user-defined class"
f._args = dict(meas=meas, schema=schema, rm_none=rm_none,
extra_tags=extra_tags, placeholder=placeholder)
return f | [
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19,764 | gusutabopb/aioinflux | aioinflux/serialization/usertype.py | lineprotocol | def lineprotocol(
cls=None,
*,
schema: Optional[Mapping[str, type]] = None,
rm_none: bool = False,
extra_tags: Optional[Mapping[str, str]] = None,
placeholder: bool = False
):
"""Adds ``to_lineprotocol`` method to arbitrary user-defined classes
:param cls: Class to monkey-patch
:param schema: Schema dictionary (attr/type pairs).
:param rm_none: Whether apply a regex to remove ``None`` values.
If ``False``, passing ``None`` values to boolean, integer or float or time fields
will result in write errors. Setting to ``True`` is "safer" but impacts performance.
:param extra_tags: Hard coded tags to be added to every point generated.
:param placeholder: If no field attributes are present, add a placeholder attribute (``_``)
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(which is not supported natively by InfluxDB)
"""
def _lineprotocol(cls):
_schema = schema or getattr(cls, '__annotations__', {})
f = _make_serializer(cls.__name__, _schema, rm_none, extra_tags, placeholder)
cls.to_lineprotocol = f
return cls
return _lineprotocol(cls) if cls else _lineprotocol | python | def lineprotocol(
cls=None,
*,
schema: Optional[Mapping[str, type]] = None,
rm_none: bool = False,
extra_tags: Optional[Mapping[str, str]] = None,
placeholder: bool = False
):
def _lineprotocol(cls):
_schema = schema or getattr(cls, '__annotations__', {})
f = _make_serializer(cls.__name__, _schema, rm_none, extra_tags, placeholder)
cls.to_lineprotocol = f
return cls
return _lineprotocol(cls) if cls else _lineprotocol | [
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19,765 | gusutabopb/aioinflux | aioinflux/serialization/mapping.py | _serialize_fields | def _serialize_fields(point):
"""Field values can be floats, integers, strings, or Booleans."""
output = []
for k, v in point['fields'].items():
k = escape(k, key_escape)
if isinstance(v, bool):
output.append(f'{k}={v}')
elif isinstance(v, int):
output.append(f'{k}={v}i')
elif isinstance(v, str):
output.append(f'{k}="{v.translate(str_escape)}"')
elif v is None:
# Empty values
continue
else:
# Floats
output.append(f'{k}={v}')
return ','.join(output) | python | def _serialize_fields(point):
output = []
for k, v in point['fields'].items():
k = escape(k, key_escape)
if isinstance(v, bool):
output.append(f'{k}={v}')
elif isinstance(v, int):
output.append(f'{k}={v}i')
elif isinstance(v, str):
output.append(f'{k}="{v.translate(str_escape)}"')
elif v is None:
# Empty values
continue
else:
# Floats
output.append(f'{k}={v}')
return ','.join(output) | [
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19,766 | gusutabopb/aioinflux | aioinflux/serialization/__init__.py | serialize | def serialize(data, measurement=None, tag_columns=None, **extra_tags):
"""Converts input data into line protocol format"""
if isinstance(data, bytes):
return data
elif isinstance(data, str):
return data.encode('utf-8')
elif hasattr(data, 'to_lineprotocol'):
return data.to_lineprotocol()
elif pd is not None and isinstance(data, pd.DataFrame):
return dataframe.serialize(data, measurement, tag_columns, **extra_tags)
elif isinstance(data, dict):
return mapping.serialize(data, measurement, **extra_tags)
elif hasattr(data, '__iter__'):
return b'\n'.join([serialize(i, measurement, tag_columns, **extra_tags) for i in data])
else:
raise ValueError('Invalid input', data) | python | def serialize(data, measurement=None, tag_columns=None, **extra_tags):
if isinstance(data, bytes):
return data
elif isinstance(data, str):
return data.encode('utf-8')
elif hasattr(data, 'to_lineprotocol'):
return data.to_lineprotocol()
elif pd is not None and isinstance(data, pd.DataFrame):
return dataframe.serialize(data, measurement, tag_columns, **extra_tags)
elif isinstance(data, dict):
return mapping.serialize(data, measurement, **extra_tags)
elif hasattr(data, '__iter__'):
return b'\n'.join([serialize(i, measurement, tag_columns, **extra_tags) for i in data])
else:
raise ValueError('Invalid input', data) | [
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19,767 | gusutabopb/aioinflux | aioinflux/iterutils.py | iterpoints | def iterpoints(resp: dict, parser: Optional[Callable] = None) -> Iterator[Any]:
"""Iterates a response JSON yielding data point by point.
Can be used with both regular and chunked responses.
By default, returns just a plain list of values representing each point,
without column names, or other metadata.
In case a specific format is needed, an optional ``parser`` argument can be passed.
``parser`` is a function/callable that takes data point values
and, optionally, a ``meta`` parameter containing which takes a
dictionary containing all or a subset of the following:
``{'columns', 'name', 'tags', 'statement_id'}``.
Sample parser functions:
.. code:: python
# Function optional meta argument
def parser(*x, meta):
return dict(zip(meta['columns'], x))
# Namedtuple (callable)
from collections import namedtuple
parser = namedtuple('MyPoint', ['col1', 'col2', 'col3'])
:param resp: Dictionary containing parsed JSON (output from InfluxDBClient.query)
:param parser: Optional parser function/callable
:return: Generator object
"""
for statement in resp['results']:
if 'series' not in statement:
continue
for series in statement['series']:
if parser is None:
return (x for x in series['values'])
elif 'meta' in inspect.signature(parser).parameters:
meta = {k: series[k] for k in series if k != 'values'}
meta['statement_id'] = statement['statement_id']
return (parser(*x, meta=meta) for x in series['values'])
else:
return (parser(*x) for x in series['values'])
return iter([]) | python | def iterpoints(resp: dict, parser: Optional[Callable] = None) -> Iterator[Any]:
for statement in resp['results']:
if 'series' not in statement:
continue
for series in statement['series']:
if parser is None:
return (x for x in series['values'])
elif 'meta' in inspect.signature(parser).parameters:
meta = {k: series[k] for k in series if k != 'values'}
meta['statement_id'] = statement['statement_id']
return (parser(*x, meta=meta) for x in series['values'])
else:
return (parser(*x) for x in series['values'])
return iter([]) | [
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In case a specific format is needed, an optional ``parser`` argument can be passed.
``parser`` is a function/callable that takes data point values
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Sample parser functions:
.. code:: python
# Function optional meta argument
def parser(*x, meta):
return dict(zip(meta['columns'], x))
# Namedtuple (callable)
from collections import namedtuple
parser = namedtuple('MyPoint', ['col1', 'col2', 'col3'])
:param resp: Dictionary containing parsed JSON (output from InfluxDBClient.query)
:param parser: Optional parser function/callable
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19,768 | gusutabopb/aioinflux | aioinflux/serialization/dataframe.py | parse | def parse(resp) -> DataFrameType:
"""Makes a dictionary of DataFrames from a response object"""
statements = []
for statement in resp['results']:
series = {}
for s in statement.get('series', []):
series[_get_name(s)] = _drop_zero_index(_serializer(s))
statements.append(series)
if len(statements) == 1:
series: dict = statements[0]
if len(series) == 1:
return list(series.values())[0] # DataFrame
else:
return series # dict
return statements | python | def parse(resp) -> DataFrameType:
statements = []
for statement in resp['results']:
series = {}
for s in statement.get('series', []):
series[_get_name(s)] = _drop_zero_index(_serializer(s))
statements.append(series)
if len(statements) == 1:
series: dict = statements[0]
if len(series) == 1:
return list(series.values())[0] # DataFrame
else:
return series # dict
return statements | [
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19,769 | gusutabopb/aioinflux | aioinflux/serialization/dataframe.py | _itertuples | def _itertuples(df):
"""Custom implementation of ``DataFrame.itertuples`` that
returns plain tuples instead of namedtuples. About 50% faster.
"""
cols = [df.iloc[:, k] for k in range(len(df.columns))]
return zip(df.index, *cols) | python | def _itertuples(df):
cols = [df.iloc[:, k] for k in range(len(df.columns))]
return zip(df.index, *cols) | [
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19,770 | gusutabopb/aioinflux | aioinflux/serialization/dataframe.py | serialize | def serialize(df, measurement, tag_columns=None, **extra_tags) -> bytes:
"""Converts a Pandas DataFrame into line protocol format"""
# Pre-processing
if measurement is None:
raise ValueError("Missing 'measurement'")
if not isinstance(df.index, pd.DatetimeIndex):
raise ValueError('DataFrame index is not DatetimeIndex')
tag_columns = set(tag_columns or [])
isnull = df.isnull().any(axis=1)
# Make parser function
tags = []
fields = []
for k, v in extra_tags.items():
tags.append(f"{k}={escape(v, key_escape)}")
for i, (k, v) in enumerate(df.dtypes.items()):
k = k.translate(key_escape)
if k in tag_columns:
tags.append(f"{k}={{p[{i+1}]}}")
elif issubclass(v.type, np.integer):
fields.append(f"{k}={{p[{i+1}]}}i")
elif issubclass(v.type, (np.float, np.bool_)):
fields.append(f"{k}={{p[{i+1}]}}")
else:
# String escaping is skipped for performance reasons
# Strings containing double-quotes can cause strange write errors
# and should be sanitized by the user.
# e.g., df[k] = df[k].astype('str').str.translate(str_escape)
fields.append(f"{k}=\"{{p[{i+1}]}}\"")
fmt = (f'{measurement}', f'{"," if tags else ""}', ','.join(tags),
' ', ','.join(fields), ' {p[0].value}')
f = eval("lambda p: f'{}'".format(''.join(fmt)))
# Map/concat
if isnull.any():
lp = map(f, _itertuples(df[~isnull]))
rep = _replace(df)
lp_nan = (reduce(lambda a, b: re.sub(*b, a), rep, f(p))
for p in _itertuples(df[isnull]))
return '\n'.join(chain(lp, lp_nan)).encode('utf-8')
else:
return '\n'.join(map(f, _itertuples(df))).encode('utf-8') | python | def serialize(df, measurement, tag_columns=None, **extra_tags) -> bytes:
# Pre-processing
if measurement is None:
raise ValueError("Missing 'measurement'")
if not isinstance(df.index, pd.DatetimeIndex):
raise ValueError('DataFrame index is not DatetimeIndex')
tag_columns = set(tag_columns or [])
isnull = df.isnull().any(axis=1)
# Make parser function
tags = []
fields = []
for k, v in extra_tags.items():
tags.append(f"{k}={escape(v, key_escape)}")
for i, (k, v) in enumerate(df.dtypes.items()):
k = k.translate(key_escape)
if k in tag_columns:
tags.append(f"{k}={{p[{i+1}]}}")
elif issubclass(v.type, np.integer):
fields.append(f"{k}={{p[{i+1}]}}i")
elif issubclass(v.type, (np.float, np.bool_)):
fields.append(f"{k}={{p[{i+1}]}}")
else:
# String escaping is skipped for performance reasons
# Strings containing double-quotes can cause strange write errors
# and should be sanitized by the user.
# e.g., df[k] = df[k].astype('str').str.translate(str_escape)
fields.append(f"{k}=\"{{p[{i+1}]}}\"")
fmt = (f'{measurement}', f'{"," if tags else ""}', ','.join(tags),
' ', ','.join(fields), ' {p[0].value}')
f = eval("lambda p: f'{}'".format(''.join(fmt)))
# Map/concat
if isnull.any():
lp = map(f, _itertuples(df[~isnull]))
rep = _replace(df)
lp_nan = (reduce(lambda a, b: re.sub(*b, a), rep, f(p))
for p in _itertuples(df[isnull]))
return '\n'.join(chain(lp, lp_nan)).encode('utf-8')
else:
return '\n'.join(map(f, _itertuples(df))).encode('utf-8') | [
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19,771 | gusutabopb/aioinflux | aioinflux/client.py | runner | def runner(coro):
"""Function execution decorator."""
@wraps(coro)
def inner(self, *args, **kwargs):
if self.mode == 'async':
return coro(self, *args, **kwargs)
return self._loop.run_until_complete(coro(self, *args, **kwargs))
return inner | python | def runner(coro):
@wraps(coro)
def inner(self, *args, **kwargs):
if self.mode == 'async':
return coro(self, *args, **kwargs)
return self._loop.run_until_complete(coro(self, *args, **kwargs))
return inner | [
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19,772 | gusutabopb/aioinflux | aioinflux/client.py | InfluxDBClient._check_error | def _check_error(response):
"""Checks for JSON error messages and raises Python exception"""
if 'error' in response:
raise InfluxDBError(response['error'])
elif 'results' in response:
for statement in response['results']:
if 'error' in statement:
msg = '{d[error]} (statement {d[statement_id]})'
raise InfluxDBError(msg.format(d=statement)) | python | def _check_error(response):
if 'error' in response:
raise InfluxDBError(response['error'])
elif 'results' in response:
for statement in response['results']:
if 'error' in statement:
msg = '{d[error]} (statement {d[statement_id]})'
raise InfluxDBError(msg.format(d=statement)) | [
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19,773 | remcohaszing/pywakeonlan | wakeonlan.py | create_magic_packet | def create_magic_packet(macaddress):
"""
Create a magic packet.
A magic packet is a packet that can be used with the for wake on lan
protocol to wake up a computer. The packet is constructed from the
mac address given as a parameter.
Args:
macaddress (str): the mac address that should be parsed into a
magic packet.
"""
if len(macaddress) == 12:
pass
elif len(macaddress) == 17:
sep = macaddress[2]
macaddress = macaddress.replace(sep, '')
else:
raise ValueError('Incorrect MAC address format')
# Pad the synchronization stream
data = b'FFFFFFFFFFFF' + (macaddress * 16).encode()
send_data = b''
# Split up the hex values in pack
for i in range(0, len(data), 2):
send_data += struct.pack(b'B', int(data[i: i + 2], 16))
return send_data | python | def create_magic_packet(macaddress):
if len(macaddress) == 12:
pass
elif len(macaddress) == 17:
sep = macaddress[2]
macaddress = macaddress.replace(sep, '')
else:
raise ValueError('Incorrect MAC address format')
# Pad the synchronization stream
data = b'FFFFFFFFFFFF' + (macaddress * 16).encode()
send_data = b''
# Split up the hex values in pack
for i in range(0, len(data), 2):
send_data += struct.pack(b'B', int(data[i: i + 2], 16))
return send_data | [
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19,774 | remcohaszing/pywakeonlan | wakeonlan.py | send_magic_packet | def send_magic_packet(*macs, **kwargs):
"""
Wake up computers having any of the given mac addresses.
Wake on lan must be enabled on the host device.
Args:
macs (str): One or more macaddresses of machines to wake.
Keyword Args:
ip_address (str): the ip address of the host to send the magic packet
to (default "255.255.255.255")
port (int): the port of the host to send the magic packet to
(default 9)
"""
packets = []
ip = kwargs.pop('ip_address', BROADCAST_IP)
port = kwargs.pop('port', DEFAULT_PORT)
for k in kwargs:
raise TypeError('send_magic_packet() got an unexpected keyword '
'argument {!r}'.format(k))
for mac in macs:
packet = create_magic_packet(mac)
packets.append(packet)
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
sock.setsockopt(socket.SOL_SOCKET, socket.SO_BROADCAST, 1)
sock.connect((ip, port))
for packet in packets:
sock.send(packet)
sock.close() | python | def send_magic_packet(*macs, **kwargs):
packets = []
ip = kwargs.pop('ip_address', BROADCAST_IP)
port = kwargs.pop('port', DEFAULT_PORT)
for k in kwargs:
raise TypeError('send_magic_packet() got an unexpected keyword '
'argument {!r}'.format(k))
for mac in macs:
packet = create_magic_packet(mac)
packets.append(packet)
sock = socket.socket(socket.AF_INET, socket.SOCK_DGRAM)
sock.setsockopt(socket.SOL_SOCKET, socket.SO_BROADCAST, 1)
sock.connect((ip, port))
for packet in packets:
sock.send(packet)
sock.close() | [
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19,775 | remcohaszing/pywakeonlan | wakeonlan.py | main | def main(argv=None):
"""
Run wake on lan as a CLI application.
"""
parser = argparse.ArgumentParser(
description='Wake one or more computers using the wake on lan'
' protocol.')
parser.add_argument(
'macs',
metavar='mac address',
nargs='+',
help='The mac addresses or of the computers you are trying to wake.')
parser.add_argument(
'-i',
metavar='ip',
default=BROADCAST_IP,
help='The ip address of the host to send the magic packet to.'
' (default {})'.format(BROADCAST_IP))
parser.add_argument(
'-p',
metavar='port',
type=int,
default=DEFAULT_PORT,
help='The port of the host to send the magic packet to (default 9)')
args = parser.parse_args(argv)
send_magic_packet(*args.macs, ip_address=args.i, port=args.p) | python | def main(argv=None):
parser = argparse.ArgumentParser(
description='Wake one or more computers using the wake on lan'
' protocol.')
parser.add_argument(
'macs',
metavar='mac address',
nargs='+',
help='The mac addresses or of the computers you are trying to wake.')
parser.add_argument(
'-i',
metavar='ip',
default=BROADCAST_IP,
help='The ip address of the host to send the magic packet to.'
' (default {})'.format(BROADCAST_IP))
parser.add_argument(
'-p',
metavar='port',
type=int,
default=DEFAULT_PORT,
help='The port of the host to send the magic packet to (default 9)')
args = parser.parse_args(argv)
send_magic_packet(*args.macs, ip_address=args.i, port=args.p) | [
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19,776 | liminspace/django-mjml | mjml/templatetags/mjml.py | mjml | def mjml(parser, token):
"""
Compile MJML template after render django template.
Usage:
{% mjml %}
.. MJML template code ..
{% endmjml %}
"""
nodelist = parser.parse(('endmjml',))
parser.delete_first_token()
tokens = token.split_contents()
if len(tokens) != 1:
raise template.TemplateSyntaxError("'%r' tag doesn't receive any arguments." % tokens[0])
return MJMLRenderNode(nodelist) | python | def mjml(parser, token):
nodelist = parser.parse(('endmjml',))
parser.delete_first_token()
tokens = token.split_contents()
if len(tokens) != 1:
raise template.TemplateSyntaxError("'%r' tag doesn't receive any arguments." % tokens[0])
return MJMLRenderNode(nodelist) | [
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{% endmjml %} | [
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19,777 | moonso/vcf_parser | vcf_parser/header_parser.py | HeaderParser.parse_header_line | def parse_header_line(self, line):
"""docstring for parse_header_line"""
self.header = line[1:].rstrip().split('\t')
if len(self.header) < 9:
self.header = line[1:].rstrip().split()
self.individuals = self.header[9:] | python | def parse_header_line(self, line):
self.header = line[1:].rstrip().split('\t')
if len(self.header) < 9:
self.header = line[1:].rstrip().split()
self.individuals = self.header[9:] | [
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19,778 | moonso/vcf_parser | vcf_parser/header_parser.py | HeaderParser.print_header | def print_header(self):
"""Returns a list with the header lines if proper format"""
lines_to_print = []
lines_to_print.append('##fileformat='+self.fileformat)
if self.filedate:
lines_to_print.append('##fileformat='+self.fileformat)
for filt in self.filter_dict:
lines_to_print.append(self.filter_dict[filt])
for form in self.format_dict:
lines_to_print.append(self.format_dict[form])
for info in self.info_dict:
lines_to_print.append(self.info_dict[info])
for contig in self.contig_dict:
lines_to_print.append(self.contig_dict[contig])
for alt in self.alt_dict:
lines_to_print.append(self.alt_dict[alt])
for other in self.other_dict:
lines_to_print.append(self.other_dict[other])
lines_to_print.append('#'+ '\t'.join(self.header))
return lines_to_print | python | def print_header(self):
lines_to_print = []
lines_to_print.append('##fileformat='+self.fileformat)
if self.filedate:
lines_to_print.append('##fileformat='+self.fileformat)
for filt in self.filter_dict:
lines_to_print.append(self.filter_dict[filt])
for form in self.format_dict:
lines_to_print.append(self.format_dict[form])
for info in self.info_dict:
lines_to_print.append(self.info_dict[info])
for contig in self.contig_dict:
lines_to_print.append(self.contig_dict[contig])
for alt in self.alt_dict:
lines_to_print.append(self.alt_dict[alt])
for other in self.other_dict:
lines_to_print.append(self.other_dict[other])
lines_to_print.append('#'+ '\t'.join(self.header))
return lines_to_print | [
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19,779 | moonso/vcf_parser | vcf_parser/parser.py | VCFParser.add_variant | def add_variant(self, chrom, pos, rs_id, ref, alt, qual, filt, info, form=None, genotypes=[]):
"""
Add a variant to the parser.
This function is for building a vcf. It takes the relevant parameters
and make a vcf variant in the proper format.
"""
variant_info = [chrom, pos, rs_id, ref, alt, qual, filt, info]
if form:
variant_info.append(form)
for individual in genotypes:
variant_info.append(individual)
variant_line = '\t'.join(variant_info)
variant = format_variant(
line = variant_line,
header_parser = self.metadata,
check_info = self.check_info
)
if not (self.split_variants and len(variant['ALT'].split(',')) > 1):
self.variants.append(variant)
# If multiple alternative and split_variants we must split the variant
else:
for splitted_variant in split_variants(
variant_dict=variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
self.variants.append(splitted_variant) | python | def add_variant(self, chrom, pos, rs_id, ref, alt, qual, filt, info, form=None, genotypes=[]):
variant_info = [chrom, pos, rs_id, ref, alt, qual, filt, info]
if form:
variant_info.append(form)
for individual in genotypes:
variant_info.append(individual)
variant_line = '\t'.join(variant_info)
variant = format_variant(
line = variant_line,
header_parser = self.metadata,
check_info = self.check_info
)
if not (self.split_variants and len(variant['ALT'].split(',')) > 1):
self.variants.append(variant)
# If multiple alternative and split_variants we must split the variant
else:
for splitted_variant in split_variants(
variant_dict=variant,
header_parser=self.metadata,
allele_symbol=self.allele_symbol):
self.variants.append(splitted_variant) | [
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19,780 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.content_get | def content_get(self, cid, nid=None):
"""Get data from post `cid` in network `nid`
:type nid: str
:param nid: This is the ID of the network (or class) from which
to query posts. This is optional and only to override the existing
`network_id` entered when created the class
:type cid: str|int
:param cid: This is the post ID which we grab
:returns: Python object containing returned data
"""
r = self.request(
method="content.get",
data={"cid": cid},
nid=nid
)
return self._handle_error(r, "Could not get post {}.".format(cid)) | python | def content_get(self, cid, nid=None):
r = self.request(
method="content.get",
data={"cid": cid},
nid=nid
)
return self._handle_error(r, "Could not get post {}.".format(cid)) | [
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19,781 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.content_create | def content_create(self, params):
"""Create a post or followup.
:type params: dict
:param params: A dict of options to pass to the endpoint. Depends on
the specific type of content being created.
:returns: Python object containing returned data
"""
r = self.request(
method="content.create",
data=params
)
return self._handle_error(
r,
"Could not create object {}.".format(repr(params))
) | python | def content_create(self, params):
r = self.request(
method="content.create",
data=params
)
return self._handle_error(
r,
"Could not create object {}.".format(repr(params))
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19,782 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.add_students | def add_students(self, student_emails, nid=None):
"""Enroll students in a network `nid`.
Piazza will email these students with instructions to
activate their account.
:type student_emails: list of str
:param student_emails: A listing of email addresses to enroll
in the network (or class). This can be a list of length one.
:type nid: str
:param nid: This is the ID of the network to add students
to. This is optional and only to override the existing
`network_id` entered when created the class
:returns: Python object containing returned data, a list
of dicts of user data of all of the users in the network
including the ones that were just added.
"""
r = self.request(
method="network.update",
data={
"from": "ClassSettingsPage",
"add_students": student_emails
},
nid=nid,
nid_key="id"
)
return self._handle_error(r, "Could not add users.") | python | def add_students(self, student_emails, nid=None):
r = self.request(
method="network.update",
data={
"from": "ClassSettingsPage",
"add_students": student_emails
},
nid=nid,
nid_key="id"
)
return self._handle_error(r, "Could not add users.") | [
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19,783 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.get_all_users | def get_all_users(self, nid=None):
"""Get a listing of data for each user in a network `nid`
:type nid: str
:param nid: This is the ID of the network to get users
from. This is optional and only to override the existing
`network_id` entered when created the class
:returns: Python object containing returned data, a list
of dicts containing user data.
"""
r = self.request(
method="network.get_all_users",
nid=nid
)
return self._handle_error(r, "Could not get users.") | python | def get_all_users(self, nid=None):
r = self.request(
method="network.get_all_users",
nid=nid
)
return self._handle_error(r, "Could not get users.") | [
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:type nid: str
:param nid: This is the ID of the network to get users
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`network_id` entered when created the class
:returns: Python object containing returned data, a list
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19,784 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.get_users | def get_users(self, user_ids, nid=None):
"""Get a listing of data for specific users `user_ids` in
a network `nid`
:type user_ids: list of str
:param user_ids: a list of user ids. These are the same
ids that are returned by get_all_users.
:type nid: str
:param nid: This is the ID of the network to get students
from. This is optional and only to override the existing
`network_id` entered when created the class
:returns: Python object containing returned data, a list
of dicts containing user data.
"""
r = self.request(
method="network.get_users",
data={"ids": user_ids},
nid=nid
)
return self._handle_error(r, "Could not get users.") | python | def get_users(self, user_ids, nid=None):
r = self.request(
method="network.get_users",
data={"ids": user_ids},
nid=nid
)
return self._handle_error(r, "Could not get users.") | [
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19,785 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.remove_users | def remove_users(self, user_ids, nid=None):
"""Remove users from a network `nid`
:type user_ids: list of str
:param user_ids: a list of user ids. These are the same
ids that are returned by get_all_users.
:type nid: str
:param nid: This is the ID of the network to remove students
from. This is optional and only to override the existing
`network_id` entered when created the class
:returns: Python object containing returned data, a list
of dicts of user data of all of the users remaining in
the network after users are removed.
"""
r = self.request(
method="network.update",
data={"remove_users": user_ids},
nid=nid,
nid_key="id"
)
return self._handle_error(r, "Could not remove users.") | python | def remove_users(self, user_ids, nid=None):
r = self.request(
method="network.update",
data={"remove_users": user_ids},
nid=nid,
nid_key="id"
)
return self._handle_error(r, "Could not remove users.") | [
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19,786 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.get_my_feed | def get_my_feed(self, limit=150, offset=20, sort="updated", nid=None):
"""Get my feed
:type limit: int
:param limit: Number of posts from feed to get, starting from ``offset``
:type offset: int
:param offset: Offset starting from bottom of feed
:type sort: str
:param sort: How to sort feed that will be retrieved; only current
known value is "updated"
:type nid: str
:param nid: This is the ID of the network to get the feed
from. This is optional and only to override the existing
`network_id` entered when created the class
"""
r = self.request(
method="network.get_my_feed",
nid=nid,
data=dict(
limit=limit,
offset=offset,
sort=sort
)
)
return self._handle_error(r, "Could not retrieve your feed.") | python | def get_my_feed(self, limit=150, offset=20, sort="updated", nid=None):
r = self.request(
method="network.get_my_feed",
nid=nid,
data=dict(
limit=limit,
offset=offset,
sort=sort
)
)
return self._handle_error(r, "Could not retrieve your feed.") | [
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19,787 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.filter_feed | def filter_feed(self, updated=False, following=False, folder=False,
filter_folder="", sort="updated", nid=None):
"""Get filtered feed
Only one filter type (updated, following, folder) is possible.
:type nid: str
:param nid: This is the ID of the network to get the feed
from. This is optional and only to override the existing
`network_id` entered when created the class
:type sort: str
:param sort: How to sort feed that will be retrieved; only current
known value is "updated"
:type updated: bool
:param updated: Set to filter through only posts which have been updated
since you last read them
:type following: bool
:param following: Set to filter through only posts which you are
following
:type folder: bool
:param folder: Set to filter through only posts which are in the
provided ``filter_folder``
:type filter_folder: str
:param filter_folder: Name of folder to show posts from; required
only if ``folder`` is set
"""
assert sum([updated, following, folder]) == 1
if folder:
assert filter_folder
if updated:
filter_type = dict(updated=1)
elif following:
filter_type = dict(following=1)
else:
filter_type = dict(folder=1, filter_folder=filter_folder)
r = self.request(
nid=nid,
method="network.filter_feed",
data=dict(
sort=sort,
**filter_type
)
)
return self._handle_error(r, "Could not retrieve filtered feed.") | python | def filter_feed(self, updated=False, following=False, folder=False,
filter_folder="", sort="updated", nid=None):
assert sum([updated, following, folder]) == 1
if folder:
assert filter_folder
if updated:
filter_type = dict(updated=1)
elif following:
filter_type = dict(following=1)
else:
filter_type = dict(folder=1, filter_folder=filter_folder)
r = self.request(
nid=nid,
method="network.filter_feed",
data=dict(
sort=sort,
**filter_type
)
)
return self._handle_error(r, "Could not retrieve filtered feed.") | [
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19,788 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.search | def search(self, query, nid=None):
"""Search for posts with ``query``
:type nid: str
:param nid: This is the ID of the network to get the feed
from. This is optional and only to override the existing
`network_id` entered when created the class
:type query: str
:param query: The search query; should just be keywords for posts
that you are looking for
"""
r = self.request(
method="network.search",
nid=nid,
data=dict(query=query)
)
return self._handle_error(r, "Search with query '{}' failed."
.format(query)) | python | def search(self, query, nid=None):
r = self.request(
method="network.search",
nid=nid,
data=dict(query=query)
)
return self._handle_error(r, "Search with query '{}' failed."
.format(query)) | [
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19,789 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.get_stats | def get_stats(self, nid=None):
"""Get statistics for class
:type nid: str
:param nid: This is the ID of the network to get stats
from. This is optional and only to override the existing
`network_id` entered when created the class
"""
r = self.request(
api_type="main",
method="network.get_stats",
nid=nid,
)
return self._handle_error(r, "Could not retrieve stats for class.") | python | def get_stats(self, nid=None):
r = self.request(
api_type="main",
method="network.get_stats",
nid=nid,
)
return self._handle_error(r, "Could not retrieve stats for class.") | [
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19,790 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC.request | def request(self, method, data=None, nid=None, nid_key='nid',
api_type="logic", return_response=False):
"""Get data from arbitrary Piazza API endpoint `method` in network `nid`
:type method: str
:param method: An internal Piazza API method name like `content.get`
or `network.get_users`
:type data: dict
:param data: Key-value data to pass to Piazza in the request
:type nid: str
:param nid: This is the ID of the network to which the request
should be made. This is optional and only to override the
existing `network_id` entered when creating the class
:type nid_key: str
:param nid_key: Name expected by Piazza for `nid` when making request.
(Usually and by default "nid", but sometimes "id" is expected)
:returns: Python object containing returned data
:type return_response: bool
:param return_response: If set, returns whole :class:`requests.Response`
object rather than just the response body
"""
self._check_authenticated()
nid = nid if nid else self._nid
if data is None:
data = {}
headers = {}
if "session_id" in self.session.cookies:
headers["CSRF-Token"] = self.session.cookies["session_id"]
# Adding a nonce to the request
endpoint = self.base_api_urls[api_type]
if api_type == "logic":
endpoint += "?method={}&aid={}".format(
method,
_piazza_nonce()
)
response = self.session.post(
endpoint,
data=json.dumps({
"method": method,
"params": dict({nid_key: nid}, **data)
}),
headers=headers
)
return response if return_response else response.json() | python | def request(self, method, data=None, nid=None, nid_key='nid',
api_type="logic", return_response=False):
self._check_authenticated()
nid = nid if nid else self._nid
if data is None:
data = {}
headers = {}
if "session_id" in self.session.cookies:
headers["CSRF-Token"] = self.session.cookies["session_id"]
# Adding a nonce to the request
endpoint = self.base_api_urls[api_type]
if api_type == "logic":
endpoint += "?method={}&aid={}".format(
method,
_piazza_nonce()
)
response = self.session.post(
endpoint,
data=json.dumps({
"method": method,
"params": dict({nid_key: nid}, **data)
}),
headers=headers
)
return response if return_response else response.json() | [
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19,791 | hfaran/piazza-api | piazza_api/rpc.py | PiazzaRPC._handle_error | def _handle_error(self, result, err_msg):
"""Check result for error
:type result: dict
:param result: response body
:type err_msg: str
:param err_msg: The message given to the :class:`RequestError` instance
raised
:returns: Actual result from result
:raises RequestError: If result has error
"""
if result.get(u'error'):
raise RequestError("{}\nResponse: {}".format(
err_msg,
json.dumps(result, indent=2)
))
else:
return result.get(u'result') | python | def _handle_error(self, result, err_msg):
if result.get(u'error'):
raise RequestError("{}\nResponse: {}".format(
err_msg,
json.dumps(result, indent=2)
))
else:
return result.get(u'result') | [
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19,792 | hfaran/piazza-api | piazza_api/piazza.py | Piazza.get_user_classes | def get_user_classes(self):
"""Get list of the current user's classes. This is a subset of the
information returned by the call to ``get_user_status``.
:returns: Classes of currently authenticated user
:rtype: list
"""
# Previously getting classes from profile (such a list is incomplete)
# raw_classes = self.get_user_profile().get('all_classes').values()
# Get classes from the user status (includes all classes)
status = self.get_user_status()
uid = status['id']
raw_classes = status.get('networks', [])
classes = []
for rawc in raw_classes:
c = {k: rawc[k] for k in ['name', 'term']}
c['num'] = rawc.get('course_number', '')
c['nid'] = rawc['id']
c['is_ta'] = uid in rawc['prof_hash']
classes.append(c)
return classes | python | def get_user_classes(self):
# Previously getting classes from profile (such a list is incomplete)
# raw_classes = self.get_user_profile().get('all_classes').values()
# Get classes from the user status (includes all classes)
status = self.get_user_status()
uid = status['id']
raw_classes = status.get('networks', [])
classes = []
for rawc in raw_classes:
c = {k: rawc[k] for k in ['name', 'term']}
c['num'] = rawc.get('course_number', '')
c['nid'] = rawc['id']
c['is_ta'] = uid in rawc['prof_hash']
classes.append(c)
return classes | [
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19,793 | hfaran/piazza-api | piazza_api/nonce.py | nonce | def nonce():
"""
Returns a new nonce to be used with the Piazza API.
"""
nonce_part1 = _int2base(int(_time()*1000), 36)
nonce_part2 = _int2base(round(_random()*1679616), 36)
return "{}{}".format(nonce_part1, nonce_part2) | python | def nonce():
nonce_part1 = _int2base(int(_time()*1000), 36)
nonce_part2 = _int2base(round(_random()*1679616), 36)
return "{}{}".format(nonce_part1, nonce_part2) | [
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19,794 | hfaran/piazza-api | piazza_api/network.py | Network.iter_all_posts | def iter_all_posts(self, limit=None):
"""Get all posts visible to the current user
This grabs you current feed and ids of all posts from it; each post
is then individually fetched. This method does not go against
a bulk endpoint; it retrieves each post individually, so a
caution to the user when using this.
:type limit: int|None
:param limit: If given, will limit the number of posts to fetch
before the generator is exhausted and raises StopIteration.
No special consideration is given to `0`; provide `None` to
retrieve all posts.
:returns: An iterator which yields all posts which the current user
can view
:rtype: generator
"""
feed = self.get_feed(limit=999999, offset=0)
cids = [post['id'] for post in feed["feed"]]
if limit is not None:
cids = cids[:limit]
for cid in cids:
yield self.get_post(cid) | python | def iter_all_posts(self, limit=None):
feed = self.get_feed(limit=999999, offset=0)
cids = [post['id'] for post in feed["feed"]]
if limit is not None:
cids = cids[:limit]
for cid in cids:
yield self.get_post(cid) | [
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19,795 | hfaran/piazza-api | piazza_api/network.py | Network.create_post | def create_post(self, post_type, post_folders, post_subject, post_content, is_announcement=0, bypass_email=0, anonymous=False):
"""Create a post
It seems like if the post has `<p>` tags, then it's treated as HTML,
but is treated as text otherwise. You'll want to provide `content`
accordingly.
:type post_type: str
:param post_type: 'note', 'question'
:type post_folders: str
:param post_folders: Folder to put post into
:type post_subject: str
:param post_subject: Subject string
:type post_content: str
:param post_content: Content string
:type is_announcement: bool
:param is_announcement:
:type bypass_email: bool
:param bypass_email:
:type anonymous: bool
:param anonymous:
:rtype: dict
:returns: Dictionary with information about the created post.
"""
params = {
"anonymous": "yes" if anonymous else "no",
"subject": post_subject,
"content": post_content,
"folders": post_folders,
"type": post_type,
"config": {
"bypass_email": bypass_email,
"is_announcement": is_announcement
}
}
return self._rpc.content_create(params) | python | def create_post(self, post_type, post_folders, post_subject, post_content, is_announcement=0, bypass_email=0, anonymous=False):
params = {
"anonymous": "yes" if anonymous else "no",
"subject": post_subject,
"content": post_content,
"folders": post_folders,
"type": post_type,
"config": {
"bypass_email": bypass_email,
"is_announcement": is_announcement
}
}
return self._rpc.content_create(params) | [
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19,796 | hfaran/piazza-api | piazza_api/network.py | Network.create_followup | def create_followup(self, post, content, anonymous=False):
"""Create a follow-up on a post `post`.
It seems like if the post has `<p>` tags, then it's treated as HTML,
but is treated as text otherwise. You'll want to provide `content`
accordingly.
:type post: dict|str|int
:param post: Either the post dict returned by another API method, or
the `cid` field of that post.
:type content: str
:param content: The content of the followup.
:type anonymous: bool
:param anonymous: Whether or not to post anonymously.
:rtype: dict
:returns: Dictionary with information about the created follow-up.
"""
try:
cid = post["id"]
except KeyError:
cid = post
params = {
"cid": cid,
"type": "followup",
# For followups, the content is actually put into the subject.
"subject": content,
"content": "",
"anonymous": "yes" if anonymous else "no",
}
return self._rpc.content_create(params) | python | def create_followup(self, post, content, anonymous=False):
try:
cid = post["id"]
except KeyError:
cid = post
params = {
"cid": cid,
"type": "followup",
# For followups, the content is actually put into the subject.
"subject": content,
"content": "",
"anonymous": "yes" if anonymous else "no",
}
return self._rpc.content_create(params) | [
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:param post: Either the post dict returned by another API method, or
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:type content: str
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:param anonymous: Whether or not to post anonymously.
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19,797 | hfaran/piazza-api | piazza_api/network.py | Network.create_instructor_answer | def create_instructor_answer(self, post, content, revision, anonymous=False):
"""Create an instructor's answer to a post `post`.
It seems like if the post has `<p>` tags, then it's treated as HTML,
but is treated as text otherwise. You'll want to provide `content`
accordingly.
:type post: dict|str|int
:param post: Either the post dict returned by another API method, or
the `cid` field of that post.
:type content: str
:param content: The content of the answer.
:type revision: int
:param revision: The number of revisions the answer has gone through.
The first responder should out 0, the first editor 1, etc.
:type anonymous: bool
:param anonymous: Whether or not to post anonymously.
:rtype: dict
:returns: Dictionary with information about the created answer.
"""
try:
cid = post["id"]
except KeyError:
cid = post
params = {
"cid": cid,
"type": "i_answer",
"content": content,
"revision": revision,
"anonymous": "yes" if anonymous else "no",
}
return self._rpc.content_instructor_answer(params) | python | def create_instructor_answer(self, post, content, revision, anonymous=False):
try:
cid = post["id"]
except KeyError:
cid = post
params = {
"cid": cid,
"type": "i_answer",
"content": content,
"revision": revision,
"anonymous": "yes" if anonymous else "no",
}
return self._rpc.content_instructor_answer(params) | [
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:type post: dict|str|int
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19,798 | hfaran/piazza-api | piazza_api/network.py | Network.mark_as_duplicate | def mark_as_duplicate(self, duplicated_cid, master_cid, msg=''):
"""Mark the post at ``duplicated_cid`` as a duplicate of ``master_cid``
:type duplicated_cid: int
:param duplicated_cid: The numeric id of the duplicated post
:type master_cid: int
:param master_cid: The numeric id of an older post. This will be the
post that gets kept and ``duplicated_cid`` post will be concatinated
as a follow up to ``master_cid`` post.
:type msg: string
:param msg: the optional message (or reason for marking as duplicate)
:returns: True if it is successful. False otherwise
"""
content_id_from = self.get_post(duplicated_cid)["id"]
content_id_to = self.get_post(master_cid)["id"]
params = {
"cid_dupe": content_id_from,
"cid_to": content_id_to,
"msg": msg
}
return self._rpc.content_mark_duplicate(params) | python | def mark_as_duplicate(self, duplicated_cid, master_cid, msg=''):
content_id_from = self.get_post(duplicated_cid)["id"]
content_id_to = self.get_post(master_cid)["id"]
params = {
"cid_dupe": content_id_from,
"cid_to": content_id_to,
"msg": msg
}
return self._rpc.content_mark_duplicate(params) | [
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19,799 | hfaran/piazza-api | piazza_api/network.py | Network.resolve_post | def resolve_post(self, post):
"""Mark post as resolved
:type post: dict|str|int
:param post: Either the post dict returned by another API method, or
the `cid` field of that post.
:returns: True if it is successful. False otherwise
"""
try:
cid = post["id"]
except KeyError:
cid = post
params = {
"cid": cid,
"resolved": "true"
}
return self._rpc.content_mark_resolved(params) | python | def resolve_post(self, post):
try:
cid = post["id"]
except KeyError:
cid = post
params = {
"cid": cid,
"resolved": "true"
}
return self._rpc.content_mark_resolved(params) | [
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