def test_match_temporal_coverage(self):
query = QueryManager.match_temporal_coverage(start="2018-09-23", end="2018-09-30T00:00:00")
expected = {
"query": {
"nested": {
"path": "variables",
"inner_hits": {"_source": ["temporal_coverage"]},
"query": {
"bool": {
"must": [
{
"range": {
"variables.temporal_coverage.start": {
"lte": "2018-09-23T00:00:00",
"format": "yyyy-MM-dd'T'HH:mm:ss"
}
}
},
{
"range": {
"variables.temporal_coverage.end": {
"gte": "2018-09-30T00:00:00",
"format": "yyyy-MM-dd'T'HH:mm:ss"
}
}
}
]
}
}
}
}
}
self.assertEqual(json.dumps(expected), query)
def test_match_temporal_coverage_invalid(self):
query = QueryManager.match_temporal_coverage(start="2222s",
end="2018-09-30T00:00:00")
expected = {
"query": {
"bool": {
"must": [{
"range": {
"variables.temporal_coverage.end": {
"gte": "2018-09-30T00:00:00",
"format": "yyyy-MM-dd'T'HH:mm:ss"
}
}
}]
}
}
}
self.assertEqual(json.dumps(expected), query)
class Augment(object):
def __init__(self,
es_index: str,
es_host: str = "dsbox02.isi.edu",
es_port: int = 9200) -> None:
"""Init method of QuerySystem, set up connection to elastic search.
Args:
es_index: elastic search index.
es_host: es_host.
es_port: es_port.
Returns:
"""
self.qm = QueryManager(es_host=es_host,
es_port=es_port,
es_index=es_index)
self.joiners = dict()
self.profiler = Profiler()
def query(self,
col: pd.Series = None,
minimum_should_match_ratio_for_col: float = None,
query_string: str = None,
temporal_coverage_start: str = None,
temporal_coverage_end: str = None,
global_datamart_id: int = None,
variable_datamart_id: int = None,
key_value_pairs: typing.List[tuple] = None,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by a pandas Dataframe column
Args:
col: pandas Dataframe column.
minimum_should_match_ratio_for_col: An float ranges from 0 to 1
indicating the ratio of unique value of the column to be matched
query_string: string to query any field in metadata
temporal_coverage_start: start of a temporal coverage
temporal_coverage_end: end of a temporal coverage
global_datamart_id: match a global metadata id
variable_datamart_id: match a variable metadata id
key_value_pairs: match key value pairs
Returns:
matching docs of metadata
"""
queries = list()
if query_string:
queries.append(self.qm.match_any(query_string=query_string))
if temporal_coverage_start or temporal_coverage_end:
queries.append(
self.qm.match_temporal_coverage(start=temporal_coverage_start,
end=temporal_coverage_end))
if global_datamart_id:
queries.append(
self.qm.match_global_datamart_id(
datamart_id=global_datamart_id))
if variable_datamart_id:
queries.append(
self.qm.match_variable_datamart_id(
datamart_id=variable_datamart_id))
if key_value_pairs:
queries.append(
self.qm.match_key_value_pairs(key_value_pairs=key_value_pairs))
if col is not None:
queries.append(
self.qm.match_some_terms_from_variables_array(
terms=col.unique().tolist(),
minimum_should_match=minimum_should_match_ratio_for_col))
if not queries:
return self._query_all()
return self.qm.search(body=self.qm.form_conjunction_query(queries),
**kwargs)
def _query_by_es_query(self, body: str,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by an elastic search query
Args:
body: query body
Returns:
matching docs of metadata
"""
return self.qm.search(body=body, **kwargs)
def _query_all(self, **kwargs) -> typing.Optional[typing.List[dict]]:
"""Query all metadata
Args:
Returns:
matching docs of metadata
"""
return self.qm.search(body=self.qm.match_all(), **kwargs)
def join(self,
left_df: pd.DataFrame,
right_df: pd.DataFrame,
left_columns: typing.List[typing.List[int]],
right_columns: typing.List[typing.List[int]],
left_metadata: dict = None,
right_metadata: dict = None,
joiner: str = "default") -> typing.Optional[pd.DataFrame]:
"""Join two dataframes based on different joiner.
Args:
left_df: pandas Dataframe
right_df: pandas Dataframe
left_metadata: metadata of left dataframe
right_metadata: metadata of right dataframe
left_columns: list of integers from left df for join
right_columns: list of integers from right df for join
joiner: string of joiner, default to be "default"
Returns:
Dataframe
"""
if joiner not in self.joiners:
self.joiners[joiner] = JoinerPrepare.prepare_joiner(joiner=joiner)
if not self.joiners[joiner]:
warnings.warn("No suitable joiner, return original dataframe")
return left_df
if not left_metadata:
# Left df is the user provided one.
# We will generate metadata just based on the data itself, profiling and so on
left_metadata = Utils.generate_metadata_from_dataframe(
data=left_df)
left_metadata = Utils.calculate_dsbox_features(data=left_df,
metadata=left_metadata)
right_metadata = Utils.calculate_dsbox_features(
data=right_df, metadata=right_metadata)
return self.joiners[joiner].join(
left_df=left_df,
right_df=right_df,
left_columns=left_columns,
right_columns=right_columns,
left_metadata=left_metadata,
right_metadata=right_metadata,
)
class Augment(object):
def __init__(self, es_index: str, es_host: str = "dsbox02.isi.edu", es_port: int = 9200) -> None:
"""Init method of QuerySystem, set up connection to elastic search.
Args:
es_index: elastic search index.
es_host: es_host.
es_port: es_port.
Returns:
"""
self.qm = QueryManager(es_host=es_host, es_port=es_port, es_index=es_index)
def query_by_column(self,
col: pd.Series,
minimum_should_match: int = None,
**kwargs
) -> typing.Optional[typing.List[dict]]:
"""Query metadata by a pandas Dataframe column
Args:
col: pandas Dataframe column.
minimum_should_match: An integer ranges from 0 to length of unique value in col.
Represent the minimum number of terms should match.
Returns:
matching docs of metadata
"""
body = self.qm.match_some_terms_from_array(terms=col.unique().tolist(),
minimum_should_match=minimum_should_match)
return self.qm.search(body=body, **kwargs)
def query_by_named_entities(self,
named_entities: list,
minimum_should_match: int = None,
**kwargs
) -> typing.Optional[typing.List[dict]]:
"""Query metadata by a pandas Dataframe column
Args:
named_entities: list of named entities
minimum_should_match: An integer ranges from 0 to length of named entities list.
Represent the minimum number of terms should match.
Returns:
matching docs of metadata
"""
body = self.qm.match_some_terms_from_array(terms=named_entities,
key="variables.named_entity.keyword",
minimum_should_match=minimum_should_match)
return self.qm.search(body=body, **kwargs)
def query_by_temporal_coverage(self, start=None, end=None, **kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by a temporal coverage of column
Args:
start: dataset should cover date time earlier than the start date.
end: dataset should cover date time later than the end date.
Returns:
matching docs of metadata
"""
body = self.qm.match_temporal_coverage(start=start, end=end)
return self.qm.search(body=body, **kwargs)
def query_by_datamart_id(self, datamart_id: int, **kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by datamart id
Args:
datamart_id: int
Returns:
matching docs of metadata
"""
global_body = self.qm.match_global_datamart_id(datamart_id=datamart_id)
variable_body = self.qm.match_variable_datamart_id(datamart_id=datamart_id)
return self.qm.search(body=global_body, **kwargs) or self.qm.search(body=variable_body, **kwargs)
def query_by_key_value_pairs(self,
key_value_pairs: typing.List[tuple],
**kwargs
) -> typing.Optional[typing.List[dict]]:
"""Query metadata by datamart id
Args:
key_value_pairs: list of key value tuple
Returns:
matching docs of metadata
"""
body = self.qm.match_key_value_pairs(key_value_pairs=key_value_pairs)
return self.qm.search(body=body, **kwargs)
def query_any_field_with_string(self, query_string, **kwargs) -> typing.Optional[typing.List[dict]]:
"""Query any field of matadata with query_string
Args:
key_value_pairs: list of key value tuple
Returns:
matching docs of metadata
"""
body = self.qm.match_any(query_string=query_string)
return self.qm.search(body=body, **kwargs)
def query_by_es_query(self, body: str, **kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by an elastic search query
Args:
body: query body
Returns:
matching docs of metadata
"""
return self.qm.search(body=body, **kwargs)
@staticmethod
def get_dataset(metadata: dict, variables: list = None, constrains: dict = None) -> typing.Optional[pd.DataFrame]:
"""Get the dataset with materializer.
Args:
metadata: metadata dict.
variables:
constrains:
Returns:
pandas dataframe
"""
return Utils.materialize(metadata=metadata, variables=variables, constrains=constrains)
class Augment(object):
DEFAULT_START_DATE = "1900-01-01T00:00:00"
def __init__(self,
es_index: str,
es_host: str = "dsbox02.isi.edu",
es_port: int = 9200) -> None:
"""Init method of QuerySystem, set up connection to elastic search.
Args:
es_index: elastic search index.
es_host: es_host.
es_port: es_port.
Returns:
"""
self.qm = QueryManager(es_host=es_host,
es_port=es_port,
es_index=es_index)
self.joiners = dict()
def query_by_column(self,
col: pd.Series,
minimum_should_match: int = None,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by a pandas Dataframe column
Args:
col: pandas Dataframe column.
minimum_should_match: An integer ranges from 0 to length of unique value in col.
Represent the minimum number of terms should match.
Returns:
matching docs of metadata
"""
body = self.qm.match_some_terms_from_variables_array(
terms=col.unique().tolist(),
minimum_should_match=minimum_should_match)
return self.qm.search(body=body, **kwargs)
def query_by_named_entities(
self,
named_entities: list,
minimum_should_match: int = None,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by a pandas Dataframe column
Args:
named_entities: list of named entities
minimum_should_match: An integer ranges from 0 to length of named entities list.
Represent the minimum number of terms should match.
Returns:
matching docs of metadata
"""
body = self.qm.match_some_terms_from_variables_array(
terms=named_entities,
key="variables.named_entity",
minimum_should_match=minimum_should_match)
return self.qm.search(body=body, **kwargs)
def query_by_temporal_coverage(
self,
start=None,
end=None,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by a temporal coverage of column
Args:
start: dataset should cover date time earlier than the start date.
end: dataset should cover date time later than the end date.
Returns:
matching docs of metadata
"""
body = self.qm.match_temporal_coverage(start=start, end=end)
return self.qm.search(body=body, **kwargs)
def query_by_datamart_id(self, datamart_id: int,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by datamart id
Args:
datamart_id: int
Returns:
matching docs of metadata
"""
global_body = self.qm.match_global_datamart_id(datamart_id=datamart_id)
variable_body = self.qm.match_variable_datamart_id(
datamart_id=datamart_id)
return self.qm.search(body=global_body, **kwargs) or self.qm.search(
body=variable_body, **kwargs)
def query_by_key_value_pairs(
self, key_value_pairs: typing.List[tuple],
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by datamart id
Args:
key_value_pairs: list of key value tuple
Returns:
matching docs of metadata
"""
body = self.qm.match_key_value_pairs(key_value_pairs=key_value_pairs)
return self.qm.search(body=body, **kwargs)
def query_any_field_with_string(
self, query_string,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query any field of matadata with query_string
Args:
key_value_pairs: list of key value tuple
Returns:
matching docs of metadata
"""
body = self.qm.match_any(query_string=query_string)
return self.qm.search(body=body, **kwargs)
def query_by_es_query(self, body: str,
**kwargs) -> typing.Optional[typing.List[dict]]:
"""Query metadata by an elastic search query
Args:
body: query body
Returns:
matching docs of metadata
"""
return self.qm.search(body=body, **kwargs)
@staticmethod
def get_dataset(metadata: dict,
variables: list = None,
constrains: dict = None) -> typing.Optional[pd.DataFrame]:
"""Get the dataset with materializer.
Args:
metadata: metadata dict.
variables:
constrains:
Returns:
pandas dataframe
"""
if "date_range" in constrains:
if not constrains["date_range"].get("start", None):
constrains["date_range"]["start"] = Augment.DEFAULT_START_DATE
if not constrains["date_range"].get("end", None):
constrains["date_range"]["end"] = datetime.now().strftime(
'%Y-%m-%dT%H:%M:%S')
df = Utils.materialize(metadata=metadata, constrains=constrains)
if variables:
return df.iloc[:, variables]
return df
@staticmethod
def get_metadata_intersection(*metadata_lst) -> list:
"""Get the intersect metadata list.
Args:
metadata_lst: all metadata list returned by multiple queries
Returns:
list of intersect metadata
"""
metadata_dict = dict()
metadata_sets = []
for lst in metadata_lst:
this_set = set()
for x in lst:
if x["_source"]["datamart_id"] not in metadata_dict:
metadata_dict[x["_source"]["datamart_id"]] = x
this_set.add(x["_source"]["datamart_id"])
metadata_sets.append(this_set)
return [
metadata_dict[datamart_id]
for datamart_id in metadata_sets[0].intersection(
*metadata_sets[1:])
]
def join(self,
left_df: pd.DataFrame,
right_df: pd.DataFrame,
left_columns: typing.List[int],
right_columns: typing.List[int],
left_metadata: dict = None,
right_metadata: dict = None,
joiner: str = "default") -> typing.Optional[pd.DataFrame]:
"""Join two dataframes based on different joiner.
Args:
left_df: pandas Dataframe
right_df: pandas Dataframe
left_metadata: metadata of left dataframe
right_metadata: metadata of right dataframe
left_columns: list of integers from left df for join
right_columns: list of integers from right df for join
joiner: string of joiner, default to be "default"
Returns:
Dataframe
"""
if joiner not in self.joiners:
self.joiners[joiner] = JoinerPrepare.prepare_joiner(joiner=joiner)
if not self.joiners[joiner]:
warnings.warn("No suitable joiner, return original dataframe")
return left_df
return self.joiners[joiner].join(
left_df=left_df,
right_df=right_df,
left_columns=left_columns,
right_columns=right_columns,
left_metadata=left_metadata,
right_metadata=right_metadata,
)