<commit_before>#BEGIN_HEADER
import os
import sys
import shutil
import hashlib
import subprocess
import requests
import re
import traceback
import uuid
from datetime import datetime
from pprint import pprint, pformat
import numpy as np
import gzip

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_protein
from biokbase.workspace.client import Workspace as workspaceService
from requests_toolbelt import MultipartEncoder  # added
from biokbase.AbstractHandle.Client import AbstractHandle as HandleService  # added

#END_HEADER


class kb_util_dylan:
    '''
    Module Name:
    kb_util_dylan

    Module Description:
    ** A KBase module: kb_util_dylan
**
** This module contains basic utilities
    '''

    ######## WARNING FOR GEVENT USERS #######
    # Since asynchronous IO can lead to methods - even the same method -
    # interrupting each other, you must be *very* careful when using global
    # state. A method could easily clobber the state set by another while
    # the latter method is running.
    #########################################
    #BEGIN_CLASS_HEADER
    workspaceURL = None
    shockURL = None
    handleURL = None

    # target is a list for collecting log messages
    def log(self, target, message):
        # we should do something better here...
        if target is not None:
            target.append(message)
        print(message)
        sys.stdout.flush()

    def invalid_log(self, target, message):
        # we should do something better here...
        if target is not None:
            target.append(message)
        #print(message)
        #sys.stdout.flush()

    def get_single_end_read_library(self, ws_data, ws_info, forward):
        pass

    def get_feature_set_seqs(self, ws_data, ws_info):
        pass

    def get_genome_feature_seqs(self, ws_data, ws_info):
        pass

    def get_genome_set_feature_seqs(self, ws_data, ws_info):
        pass<commit_msg>added comment<commit_after>#BEGIN_HEADER
import os
import sys
import shutil
import hashlib
import subprocess
import requests
import re
import traceback
import uuid
from datetime import datetime
from pprint import pprint, pformat
import numpy as np
import gzip

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_protein
from biokbase.workspace.client import Workspace as workspaceService
from requests_toolbelt import MultipartEncoder  # added
from biokbase.AbstractHandle.Client import AbstractHandle as HandleService  # added

#END_HEADER


class kb_util_dylan:
    '''
    Module Name:
    kb_util_dylan

    Module Description:
    ** A KBase module: kb_util_dylan
**
** This module contains basic utilities
    '''

    ######## WARNING FOR GEVENT USERS #######
    # Since asynchronous IO can lead to methods - even the same method -
    # interrupting each other, you must be *very* careful when using global
    # state. A method could easily clobber the state set by another while
    # the latter method is running.
    #########################################
    #BEGIN_CLASS_HEADER
    workspaceURL = None
    shockURL = None
    handleURL = None

    # target is a list for collecting log messages
    def log(self, target, message):
        # we should do something better here...
        if target is not None:
            target.append(message)
        print(message)
        sys.stdout.flush()

    # target is a list for collecting log messages pertaining to failed validation tests  
    def invalid_log(self, target, message):
        # we should do something better here...
        if target is not None:
            target.append(message)
        #print(message)
        #sys.stdout.flush()

    def get_single_end_read_library(self, ws_data, ws_info, forward):
        pass

    def get_feature_set_seqs(self, ws_data, ws_info):
        pass

    def get_genome_feature_seqs(self, ws_data, ws_info):
        pass

    def get_genome_set_feature_seqs(self, ws_data, ws_info):
        pass
{'fraction_non_alphanumeric': 0.08101452844127062, 'fraction_numerical': 0.0, 'mean_word_length': 3.2224532224532223, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1870468', 'n_tokens_mistral': 1166, 'n_tokens_neox': 1104, 'n_words': 413}