<commit_before>"""
Reads a CSV that analyst uploads to genomic_set_upload bucket.
And insert to relevant genomic tables.
"""

import csv
import datetime
import logging
import pytz
from cloudstorage import cloudstorage_api
import clock
import config
from offline.sql_exporter import SqlExporter
from dao.genomics_dao import GenomicSetDao, GenomicSetMemberDao
from model.genomics import GenomicSet, GenomicSetMember, GenomicSetStatus, GenomicValidationStatus

_US_CENTRAL = pytz.timezone('US/Central')
_BATCH_SIZE = 1000
# The timestamp found at the end of input CSV files.
INPUT_CSV_TIME_FORMAT = '%Y-%m-%d-%H-%M-%S'
_INPUT_CSV_TIME_FORMAT_LENGTH = 18
_CSV_SUFFIX_LENGTH = 4
_RESULT_FILE_SUFFIX = 'Validation-Result'
_MAX_INPUT_AGE = datetime.timedelta(hours=24)

class DataError(RuntimeError):
  """Bad genomic data during import.

  Args:
    msg: Passed through to superclass.
    external: If True, this error should be reported to external partners (Analyst).
  """
  def __init__(self, msg, external=False):
    super(DataError, self).__init__(msg)
    self.external = external

class FileNotFoundError(RuntimeError):
  """genomic set file not found during import.

  Args:
    msg: Passed through to superclass.
  """
  def __init__(self, msg):
    super(FileNotFoundError, self).__init__(msg)


def read_genomic_set_from_bucket():
  try:
    csv_file, csv_filename, timestamp = get_last_genomic_set_file_info()
  except FileNotFoundError, e:
    logging.info(e.message)
    return None
  if _is_filename_exist(csv_filename):
    raise DataError(
      'This file %s has already been processed' % csv_filename, external=True)
  now = clock.CLOCK.now()
  if now - timestamp > _MAX_INPUT_AGE:
    logging.info('Input %r (timestamp %s UTC) is > %s h old (relative to %s UTC), not importing.'
                 % (_MAX_INPUT_AGE, csv_filename, timestamp, now))
    return None

  csv_reader = csv.DictReader(csv_file, delimiter=',')
  genomic_set_id = _save_genomic_set_from_csv(csv_reader, csv_filename, timestamp)

  return genomic_set_id

def get_last_genomic_set_file_info():
  """Finds the latest CSV & updates/inserts relevant genomic tables from its rows."""
  bucket_name = config.getSetting(config.GENOMIC_SET_BUCKET_NAME)  # raises if missing
  csv_file, csv_filename = _open_latest_genomic_set_file(bucket_name)
  timestamp = _timestamp_from_filename(csv_filename)

  return csv_file, csv_filename, timestamp

def _timestamp_from_filename(csv_filename):
  if len(csv_filename) < _INPUT_CSV_TIME_FORMAT_LENGTH + _CSV_SUFFIX_LENGTH:
    raise DataError("Can't parse time from CSV filename: %s" % csv_filename)
  time_suffix = csv_filename[len(csv_filename) - (_INPUT_CSV_TIME_FORMAT_LENGTH +
                                                  _CSV_SUFFIX_LENGTH) - 1:
                    len(csv_filename) - _CSV_SUFFIX_LENGTH]
  try:<commit_msg>genomic pipeline:put file exist check after timestamp check (#1068)<commit_after>"""
Reads a CSV that analyst uploads to genomic_set_upload bucket.
And insert to relevant genomic tables.
"""

import csv
import datetime
import logging
import pytz
from cloudstorage import cloudstorage_api
import clock
import config
from offline.sql_exporter import SqlExporter
from dao.genomics_dao import GenomicSetDao, GenomicSetMemberDao
from model.genomics import GenomicSet, GenomicSetMember, GenomicSetStatus, GenomicValidationStatus

_US_CENTRAL = pytz.timezone('US/Central')
_BATCH_SIZE = 1000
# The timestamp found at the end of input CSV files.
INPUT_CSV_TIME_FORMAT = '%Y-%m-%d-%H-%M-%S'
_INPUT_CSV_TIME_FORMAT_LENGTH = 18
_CSV_SUFFIX_LENGTH = 4
_RESULT_FILE_SUFFIX = 'Validation-Result'
_MAX_INPUT_AGE = datetime.timedelta(hours=24)

class DataError(RuntimeError):
  """Bad genomic data during import.

  Args:
    msg: Passed through to superclass.
    external: If True, this error should be reported to external partners (Analyst).
  """
  def __init__(self, msg, external=False):
    super(DataError, self).__init__(msg)
    self.external = external

class FileNotFoundError(RuntimeError):
  """genomic set file not found during import.

  Args:
    msg: Passed through to superclass.
  """
  def __init__(self, msg):
    super(FileNotFoundError, self).__init__(msg)


def read_genomic_set_from_bucket():
  try:
    csv_file, csv_filename, timestamp = get_last_genomic_set_file_info()
  except FileNotFoundError, e:
    logging.info(e.message)
    return None

  now = clock.CLOCK.now()
  if now - timestamp > _MAX_INPUT_AGE:
    logging.info('Input %r (timestamp %s UTC) is > %s h old (relative to %s UTC), not importing.'
                 % (_MAX_INPUT_AGE, csv_filename, timestamp, now))
    return None

  if _is_filename_exist(csv_filename):
    raise DataError(
      'This file %s has already been processed' % csv_filename, external=True)

  csv_reader = csv.DictReader(csv_file, delimiter=',')
  genomic_set_id = _save_genomic_set_from_csv(csv_reader, csv_filename, timestamp)

  return genomic_set_id

def get_last_genomic_set_file_info():
  """Finds the latest CSV & updates/inserts relevant genomic tables from its rows."""
  bucket_name = config.getSetting(config.GENOMIC_SET_BUCKET_NAME)  # raises if missing
  csv_file, csv_filename = _open_latest_genomic_set_file(bucket_name)
  timestamp = _timestamp_from_filename(csv_filename)

  return csv_file, csv_filename, timestamp

def _timestamp_from_filename(csv_filename):
  if len(csv_filename) < _INPUT_CSV_TIME_FORMAT_LENGTH + _CSV_SUFFIX_LENGTH:
    raise DataError("Can't parse time from CSV filename: %s" % csv_filename)
  time_suffix = csv_filename[len(csv_filename) - (_INPUT_CSV_TIME_FORMAT_LENGTH +
                                                  _CSV_SUFFIX_LENGTH) - 1:
                    len(csv_filename) - _CSV_SUFFIX_LENGTH]
  try:
{'fraction_non_alphanumeric': 0.08255289628858828, 'fraction_numerical': 0.004162330905306972, 'mean_word_length': 4.539865513928914, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6530903', 'n_tokens_mistral': 1910, 'n_tokens_neox': 1815, 'n_words': 481}