Mercurial > repos > ufz > saqc

annotate json_to_saqc_config.py @ 1:724dcbb35c9a draft default tip

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
author ufz
date Sat, 16 Aug 2025 11:43:23 +0000
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1
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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1 #!/usr/bin/env python
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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2
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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3 import json
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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4 import math
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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5 import sys
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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6
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7
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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8 def format_saqc_value_repr(value: any) -> str:
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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9 """
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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10 Konvertiert einen Python-Wert in seine korrekte String-Darstellung für die SaQC-Konfiguration.
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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11 Behandelt None, Bools, Floats (inkl. inf/nan) und Strings zentral.
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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12 """
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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13 if value is None:
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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14 return "None"
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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15 if isinstance(value, bool):
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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16 return str(value)
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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17 if isinstance(value, float):
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18 if math.isinf(value):
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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19 return "float('inf')" if value > 0 else "float('-inf')"
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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20 if math.isnan(value):
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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21 return "float('nan')"
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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22 return repr(value)
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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23 if isinstance(value, int):
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24 return str(value)
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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25 if isinstance(value, str):
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26 val_lower = value.lower()
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27 if val_lower == "inf":
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28 return "float('inf')"
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29 if val_lower == "-inf":
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30 return "float('-inf')"
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31 if val_lower == "nan":
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32 return "float('nan')"
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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33 escaped_v = value.replace("\\", "\\\\").replace('"', '\\"')
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34 return f'"{escaped_v}"'
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35 sys.stderr.write(
724dcbb35c9a planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe
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36 f"Warning: Unhandled type {type(value)}. Converting to string representation: '{str(value)}'.\n"
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37 )
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38 return repr(value)
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39
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40
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41 print("varname; function")
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42
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43 try:
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44 infile = sys.argv[1]
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45 with open(infile) as fh:
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46 params_from_galaxy = json.load(fh)
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47 except Exception as e:
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48 sys.stderr.write(
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49 f"Error opening or reading JSON file {infile}: {type(e).__name__} - {e}\n"
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50 )
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51 sys.exit(1)
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52
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53 EMPTY_STRING_IS_NONE_PARAMS = {
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54 "xscope",
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55 "yscope",
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56 "max_gap",
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57 "min_periods",
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58 "min_residuals",
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59 "min_offset",
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60 }
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61
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62 for r_method_set in params_from_galaxy.get("methods_repeat", []):
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63 method_str_for_error = "unknown_method_in_repeat"
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64 field_str_for_error = "unknown_field_in_repeat"
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65 try:
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66 method_cond_params = r_method_set.get("module_cond", {}).get("method_cond", {})
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67 if not method_cond_params:
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68 sys.stderr.write(
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69 f"Warning: Skipping a methods_repeat entry due to missing/empty method_cond: {r_method_set}\n"
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70 )
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71 continue
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72
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73 params_to_process = method_cond_params.copy()
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74
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75 method = params_to_process.pop("method_select", "unknown_method")
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76 method_str_for_error = method
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77
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78 raw_field_val = None
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79 if "field" in params_to_process:
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80 raw_field_val = params_to_process.pop("field")
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81 elif "field_repeat" in params_to_process:
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82 field_repeat_data = params_to_process.pop("field_repeat", [])
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83 if isinstance(field_repeat_data, list) and len(field_repeat_data) > 0:
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84 first_field_item = field_repeat_data[0]
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85 if isinstance(first_field_item, dict):
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86 raw_field_val = first_field_item.get("field")
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87
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88 if raw_field_val is None or str(raw_field_val).strip() == "":
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89 field_str = "undefined_field"
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90 field_str_for_error = "undefined_field (extraction failed or empty)"
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91 sys.stderr.write(
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92 f"Warning: Field name could not be determined for method '{method}'. Using '{field_str}'.\n"
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93 )
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94 else:
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95 field_str = str(raw_field_val) if not isinstance(raw_field_val, list) else ",".join(map(str, raw_field_val))
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96 field_str_for_error = field_str
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97
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98 saqc_args_dict = {}
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99 for param_key, param_value_json in params_to_process.items():
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100 if param_key.endswith("_select_type"):
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101 continue
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102
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103 actual_param_name_for_saqc = param_key
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104 current_value_for_saqc = param_value_json
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105
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106 if isinstance(param_value_json, dict) and param_key.endswith("_cond"):
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107 actual_param_name_for_saqc = param_key[:-5]
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108 value_found = False
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109 for inner_k, inner_v in param_value_json.items():
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110 if not inner_k.endswith("_select_type"):
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111 current_value_for_saqc = inner_v
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112 value_found = True
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113 break
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114 if not value_found:
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115 current_value_for_saqc = None
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116
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117 if current_value_for_saqc == "__none__":
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118 saqc_args_dict[actual_param_name_for_saqc] = None
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119 elif isinstance(current_value_for_saqc, str) and not current_value_for_saqc and actual_param_name_for_saqc in EMPTY_STRING_IS_NONE_PARAMS:
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120 saqc_args_dict[actual_param_name_for_saqc] = None
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121 else:
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122 saqc_args_dict[actual_param_name_for_saqc] = current_value_for_saqc
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123 param_strings_for_saqc_call = [
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124 f"{k_saqc}={format_saqc_value_repr(v_saqc)}"
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125 for k_saqc, v_saqc in sorted(saqc_args_dict.items())
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126 ]
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127
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128 print(
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129 f"{field_str}; {method}({', '.join(param_strings_for_saqc_call)})",
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130 flush=True,
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131 )
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132
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133 except Exception as e:
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134 sys.stderr.write(
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135 f"FATAL Error processing a method entry: {type(e).__name__} - {e}\n"
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136 )
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137 sys.stderr.write(
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138 f"Offending entry: {r_method_set}\n"
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139 )
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140 sys.stderr.write(
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141 f"Method context: {method_str_for_error}, Field context: {field_str_for_error}\n"
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142 )
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143 import traceback
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144 traceback.print_exc(file=sys.stderr)
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145 print(
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146 f"{field_str_for_error}; ERROR_PROCESSING_METHOD({method_str_for_error})",
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147 flush=True)
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148 continue