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ElasticSearchLoader-Otto.py~
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ElasticSearchLoader-Otto.py~
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__author__ = 'teohoch'
import csv
import elasticsearch
import json
import os
from time import sleep
from datetime import datetime
from astropy import units as u
import sys
import time
class ElasticSearchLoader():
"""
Class designed to load CSV Files containing to a ElasticSearch Server
"""
def __init__(self, fail_directory="", elastic_server=None):
"""
:param elastic_server: The Hostname for the ElasticSearch Server. Can be the hostname to a single Node or an
array of Hostnames.
:type elastic_server: String or Array of Strings
:param fail_file: Filename where to save the DataLines that couldn't be Uploaded
:type fail_file: String
"""
self.server = elastic_server
self.__server_connection = elasticsearch.Elasticsearch(hosts=elastic_server, sniff_on_start=True)
self.__default_index = None
self.__default_mapping = None
self.fail_directory = fail_directory
self.__number_uploaded = 0
self.index_json = '{' \
' "settings" :' \
' {' \
' "number_of_shards" : 10,' \
' "number_of_replicas" : 2' \
' },' \
' "mappings" :' \
' {' \
' "line" :' \
' {' \
' "properties" :' \
' {' \
' "Species" : {"type" : "string"},' \
' "Chemical Name" : {"type" : "string"},' \
' "Freq-MHz" : {"type" : "double"},' \
' "Freq Err" : {"type" : "double"},' \
' "Meas Freq-MHz" : {"type" : "double"},' \
' "Meas Freq Err" : {"type" : "double"},' \
' "Resolved QNs" : {"type" : "string"},' \
' "CDMS/JPL Intensity" : {"type" : "double"},' \
' "Sijmu2" : {"type" : "double"},' \
' "Sij" : {"type" : "double"},' \
' "Log10(Aij)" : {"type" : "double"},' \
' "Lovas/AST Intensity" : {"type" : "string"},' \
' "E_L (cm^-1)" : {"type" : "double"},' \
' "E_L (K)" : {"type" : "double"},' \
' "E_U (cm^-1)" : {"type" : "double"},' \
' "E_U (K)" : {"type" : "double"},' \
' "Linelist" : {"type" : "string"}' \
' }' \
' }' \
' }' \
'}'
def __upload_line(self, data, index, mapping, retries=10,):
"""
Upload a Single Line (Row) of Data to the Server
:param data: Array of Data to upload
:type data: Array of Strings
:param retries: Number of times to retry uploading before giving up
:type retries: int
:return: Return a Status Number. For Success => 0, For Connection Error => 1, For Malformation Error => 2,
Other => 3
:rtype: int
"""
success = 3
#print("Uploading " + str(data[0]) + " " + str(data[2]) + " " + str(data[3]) + " " + str(data[5]))
if len(data) >= 25:
try:
freq = float(data[3]) if data[3] else float(data[5])
freq_error = float(data[4]) if data[4] else (float(data[6]) if data[6] else None)
wavelenght = float(((freq * u.MHz).to(u.m, equivalencies=u.spectral()))/u.m)
line = {
"Species" : data[0],
"NRAO Recommended" : (data[1] =="*"),
"Chemical Name" : data[2],
"Calculated Freq" : float(data[3]) if data[3] else None,
"Calculated Freq Err" : float(data[4]) if data[4] else None,
"Meas Freq" : float(data[5]) if data[5] else None,
"Meas Freq Err" : float(data[6]) if data[6] else None,
"Resolved QNs" : data[7],
"Unresolved Quantum Numbers" : data[8],
"CDMS/JPL Intensity" : float(data[9]) if data[9] else None,
"Sijmu2" : float(data[10]) if data[10] else None,
"Sij" : float(data[11]) if data[11] else None,
"Log10(Aij)" : float(data[12]) if data[12] else None,
"Lovas/AST Intensity" : data[13],
"E_L (cm^-1)" : float(data[14]) if data[14] else None,
"E_L (K)" : float(data[15]) if data[15] else None,
"E_U (cm^-1)" : float(data[16]) if data[16] else None,
"E_U (K)" : float(data[17]) if data[17] else None,
"HFS int" : float(data[18]) if data[18] else None,
"Upper State Degeneracy" : float(data[19]) if data[19] else None,
"Molecule Tag" : float(data[20]) if data[20] else None,
"Quantum Number Code" : float(data[21]) if data[21] else None,
"Linelist" : data[22],
"Lab Ref" : data[23],
"Obs Ref" : data[24],
"Frequency" : freq,
"Frequency Error" : freq_error,
"Wavelenght" : wavelenght
}
try_count = 0
while try_count < retries:
try:
self.__server_connection.create(index, mapping, json.dumps(line))
success = 0
self.__number_uploaded = self.__number_uploaded +1
break
except (elasticsearch.ConnectionError, elasticsearch.ConnectionTimeout, elasticsearch.ElasticsearchException), ese:
try_count += 1
if try_count == retries:
print("Could not Upload DataLine, after " + str(retries) + "retries => " + str(data))
print(ese)
success = 1
else:
sleep(1 * try_count)
except Exception as e:
print "Error in Data Line -> " + str(data)
print e
success = 2
else:
print "DataLine is malformed -> " + str(data)
success = 2
return success
def upload_single_file(self, index, mapping, filename, delimiter=":", retries=10):
"""
Upload a single CSV file to the Server.
:param filename: File to upload.
:type filename: str
:param delimiter: Delimiter character used in the CSV, defaults to ":"
:type delimiter: str
:param retries: Number of retries before giving up.
:type retries: int
:param index: The index into which upload the data
:type index: str
"""
if index and mapping:
index = index.lower()
if self.__server_connection.indices.exists(index) and self.__server_connection.indices.get_mapping(index,mapping):
time = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
fails = {"1": ["connection", []], "2": ["malformed", []], "3": ["other", []]}
with open(filename) as csvfile:
data = csv.reader(csvfile, delimiter=delimiter)
first = True
for row in data:
if first:
first = False
else:
success = self.__upload_line(row, index, mapping, retries)
if success != 0:
fails[str(success)][1].append(row)
for key, value in fails.iteritems():
if len(value[1]) > 0:
fail_file = os.path.join(self.fail_directory, "Fail-" + filename.split("/")[-1] + "-" + value[0] + " " + time)
if len(value[1])>0:
with open(fail_file, "w") as f:
for row in value[1]:
f.write(row)
else:
raise elasticsearch.ConnectionError("The selected index or mapping doesn't exist!")
else:
raise ValueError("The index or the mapping to use wasn't defined!")
def __get_file_list(self, directory=os.getcwd(), ext=".csv"):
"""
Gets a list of files from a directory and subdirectory that match the specified extension
:param directory: The root directory to search in
:type directory: String
:param ext: The extension to search for
:type ext: String
:return: An array of file names
:rtype: Array of Strings
"""
f = []
for root, dirs, files in os.walk(directory):
for file in files:
if file.endswith(ext):
f.append(os.path.join(root, file))
return f
def upload_multiple_files(self,index, mapping, directory=os.getcwd(), ext=".csv", delimeter=":", retries=10):
"""
Uploads multiple CSV files from a directory to the Server.
:param directory: The root directory to search in
:type directory: String
:param ext: The extension to search for
:type ext: String
:param delimiter: Delimiter character used in the CSV, defaults to ":"
:type delimiter: String
:param retries: Number of retries before giving up.
:type retries: Integer
"""
data_files = self.__get_file_list(directory, ext)
for f in data_files:
print("Uploading File:" + f)
self.upload_single_file(index,mapping,f, delimeter, retries)
def create_index(self, index_name, index_options={}):
"""
Creates a Index in the ES. By default, it has no mappings and the default settings
:param index_name: Name of the index
:type index_name: String
:param index_options: Dictionary with the creation options,
refer to https://www.elastic.co/guide/en/elasticsearch/reference/1.6/indices-create-index.html
:type index_options: Dictionary
"""
lower_index_name = index_name.lower()
if not self.__server_connection.indices.exists(lower_index_name):
self.__server_connection.indices.create(lower_index_name, json.dumps(index_options))
def create_mapping(self, index_name, mapping_name, mapping_options):
index_to_lower = index_name.lower()
if self.__server_connection.indices.exists(index_to_lower) and not self.__server_connection.indices.get_mapping(index_to_lower, mapping_name):
self.__server_connection.indices.put_mapping(mapping_name, mapping_options, index_to_lower)
def generate_mapping(self, filename, delimiter=":"):
with open(filename) as csvfile:
data = csv.reader(csvfile, delimiter=delimiter)
header = next(data)
print(header)
# TODO Generate the mappings from the header in the CSV File
if __name__ == "__main__":
loader = ElasticSearchLoader(elastic_server="http://otto.csrg.inf.utfsm.cl:9200/")
index_options = {"settings": {"number_of_shards": 10, "number_of_replicas": 1}}
mapping_options = \
{"properties":
{
"Species" : {"type" : "string"},
"NRAO Recommended" : {"type" : "boolean"},
"Chemical Name" : {"type" :"string"},
"Calculated Freq" : {"type":"double"},
"Calculated Freq Err" : {"type":"double"},
"Meas Freq" : {"type":"double"},
"Meas Freq Err" : {"type":"double"},
"Resolved QNs" : {"type":"string"},
"Unresolved Quantum Numbers" : {"type":"string"},
"CDMS/JPL Intensity" : {"type":"string"},
"Sijmu2" : {"type":"double"},
"Sij" : {"type":"double"},
"Log10(Aij)" : {"type":"double"},
"Lovas/AST Intensity" : {"type":"double"},
"E_L(cm^-1)" : {"type":"double"},
"E_L(K)" : {"type":"double"},
"E_U(cm^-1)" : {"type":"double"},
"E_U(K)" : {"type":"double"},
"HFS int" : {"type":"double"},
"Upper State Degeneracy" : {"type":"double"},
"Molecule Tag" : {"type":"double"},
"Quantum Number Code" : {"type":"double"},
"Linelist" : {"type":"string"},
"Lab Ref" : {"type":"string"},
"Frequency" : {"type":"double"},
"Frequency Error" : {"type":"double"},
"Wavelenght" : {"type":"double"}
}
}
loader.create_index("SL-Repository", index_options)
loader.create_mapping("SL-Repository", "Spectral-Lines",mapping_options)
loader.upload_multiple_files("SL-Repository", "Spectral-Lines","/home/teohoch/Sla-Data")
#loader.generate_mapping("splatalogue 0-500000.csv")
# units = {
# "Species" : ("String", ""),
# "Chemical Name" : ("String", ""),
# "Freq-MHz" : ("Double", "Mhz"),
# "Freq Err" : ("Double", "Mhz"),
# "Meas Freq-MHz" : ("Double", "Mhz"),
# "Meas Freq Err" : ("Double", "Mhz"),
# "Resolved QNs" : ("String", ""),
# "CDMS/JPL Intensity" : ("Double", ""),
# "Sijmu2" : ("Double", "Devye"),
# "Sij" : ("Double", ""),
# "Log10(Aij)" : ("Double", "1/Sec"),
# "Lovas/AST Intensity" : ("String", ""),
# "E_L (cm^-1)" : ("Double", "1/cm"),
# "E_L (K)" : ("Double", "Kelvin"),
# "E_U (cm^-1)" : ("Double", "1/cm"),
# "E_U (K)" : ("Double", "Kelvin"),
# "Linelist" : ("String", "")
# }