starting build "d83f5c9f-9607-474e-b9f5-11a721914ec4"

FETCHSOURCE
hint: Using 'master' as the name for the initial branch. This default branch name
hint: is subject to change. To configure the initial branch name to use in all
hint: of your new repositories, which will suppress this warning, call:
hint:
hint: 	git config --global init.defaultBranch <name>
hint:
hint: Names commonly chosen instead of 'master' are 'main', 'trunk' and
hint: 'development'. The just-created branch can be renamed via this command:
hint:
hint: 	git branch -m <name>
Initialized empty Git repository in /workspace/.git/
From https://github.com/datacommonsorg/data
 * branch            3a1ff32bdf766423848be52dd4e437e32e27c7ea -> FETCH_HEAD
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HEAD is now at 3a1ff32 Merge branch 'master' into diseasesAtJensenLab
BUILD
Starting Step #0 - "python_install"
Step #0 - "python_install": Pulling image: python:3.11
Step #0 - "python_install": 3.11: Pulling from library/python
Step #0 - "python_install": 7d98d813d54f: Already exists
Step #0 - "python_install": da802df85c96: Already exists
Step #0 - "python_install": 7aadc5092c3b: Already exists
Step #0 - "python_install": ad1c7cfc347f: Already exists
Step #0 - "python_install": 754cb1613bc3: Pulling fs layer
Step #0 - "python_install": 07804c5f3526: Pulling fs layer
Step #0 - "python_install": 5fef6e32ff7c: Pulling fs layer
Step #0 - "python_install": 5fef6e32ff7c: Verifying Checksum
Step #0 - "python_install": 5fef6e32ff7c: Download complete
Step #0 - "python_install": 754cb1613bc3: Verifying Checksum
Step #0 - "python_install": 754cb1613bc3: Download complete
Step #0 - "python_install": 07804c5f3526: Verifying Checksum
Step #0 - "python_install": 07804c5f3526: Download complete
Step #0 - "python_install": 754cb1613bc3: Pull complete
Step #0 - "python_install": 07804c5f3526: Pull complete
Step #0 - "python_install": 5fef6e32ff7c: Pull complete
Step #0 - "python_install": Digest: sha256:70f1eb2927a8ef72840254b17024d3a8aa8c3c9715a625d426a2861b5899bc62
Step #0 - "python_install": Status: Downloaded newer image for python:3.11
Step #0 - "python_install": docker.io/library/python:3.11
Step #0 - "python_install": ### Installing Python requirements
Step #0 - "python_install": Installing Python requirements
Step #0 - "python_install": 
Step #0 - "python_install": [notice] A new release of pip is available: 24.0 -> 24.3.1
Step #0 - "python_install": [notice] To update, run: pip install --upgrade pip
Finished Step #0 - "python_install"
Starting Step #1 - "python_test"
Starting Step #2 - "python_format_check"
Step #1 - "python_test": Already have image (with digest): python:3.11
Step #2 - "python_format_check": Already have image (with digest): python:3.11
Step #2 - "python_format_check": ### Testing lint
Step #1 - "python_test": ### Running Python tests in util/
Step #1 - "python_test": Installing Python requirements
Step #2 - "python_format_check": Installing Python requirements
Step #1 - "python_test": 
Step #1 - "python_test": [notice] A new release of pip is available: 24.0 -> 24.3.1
Step #1 - "python_test": [notice] To update, run: pip install --upgrade pip
Step #2 - "python_format_check": 
Step #2 - "python_format_check": [notice] A new release of pip is available: 24.0 -> 24.3.1
Step #2 - "python_format_check": [notice] To update, run: pip install --upgrade pip
Step #1 - "python_test": #### Testing Python code in util/
Step #2 - "python_format_check": #### Testing Python lint
Step #1 - "python_test": test_aggregate_dict (aggregation_util_test.AggregationUtilTest.test_aggregate_dict) ... ok
Step #1 - "python_test": test_aggregate_value (aggregation_util_test.AggregationUtilTest.test_aggregate_value) ... ok
Step #1 - "python_test": test_config_map_with_override (config_map_test.TestConfigMap.test_config_map_with_override) ... ok
Step #1 - "python_test": test_load_config_file (config_map_test.TestConfigMap.test_load_config_file)
Step #1 - "python_test": Test loading of config dictionary from a file. ... ok
Step #1 - "python_test": test_set_config (config_map_test.TestConfigMap.test_set_config) ... ok
Step #1 - "python_test": test_update_config (config_map_test.TestConfigMap.test_update_config) ... ok
Step #1 - "python_test": test_add_counter (counters_test.TestCounters.test_add_counter)
Step #1 - "python_test": Verify increment and decrement counters. ... Counters:
Step #1 - "python_test":                                        test_inputs =         10
Step #1 - "python_test":                          test_process_elapsed_time =       0.00
Step #1 - "python_test":                                     test_processed =          0
Step #1 - "python_test":                                    test_start_time =     257.28
Step #1 - "python_test": ok
Step #1 - "python_test": test_counter_dict (counters_test.TestCounters.test_counter_dict)
Step #1 - "python_test": Verify counter dict is shared across counters. ... Counters:
Step #1 - "python_test":                               process_elapsed_time =       0.00
Step #1 - "python_test":                                          processed =          0
Step #1 - "python_test":                                         start_time =     257.28
Step #1 - "python_test":                                           test_ctr =          1
Step #1 - "python_test": ok
Step #1 - "python_test": test_debug_counters (counters_test.TestCounters.test_debug_counters)
Step #1 - "python_test": Verify counters with debug string suffixes. ... Counters:
Step #1 - "python_test":                                       test3_inputs =         10
Step #1 - "python_test":                           test3_inputs_test-case-2 =         10
Step #1 - "python_test":                         test3_process_elapsed_time =       0.00
Step #1 - "python_test":                                    test3_processed =          0
Step #1 - "python_test":                                   test3_start_time =     257.28
Step #1 - "python_test": ok
Step #1 - "python_test": test_set_counter (counters_test.TestCounters.test_set_counter)
Step #1 - "python_test": Verify set_counter overrides current value. ... Counters:
Step #1 - "python_test":                                        test2_lines =          1
Step #1 - "python_test":                                  test2_lines_file1 =          1
Step #1 - "python_test":                         test2_process_elapsed_time =       0.00
Step #1 - "python_test":                                    test2_processed =          0
Step #1 - "python_test":                                   test2_start_time =     257.28
Step #1 - "python_test": Counters:
Step #1 - "python_test":                                        test2_lines =         11
Step #1 - "python_test":                                  test2_lines_file1 =         11
Step #1 - "python_test":                         test2_process_elapsed_time =       0.00
Step #1 - "python_test":                                    test2_processed =          0
Step #1 - "python_test":                                   test2_start_time =     257.28
Step #1 - "python_test": ok
Step #1 - "python_test": test_show_counters (counters_test.TestCounters.test_show_counters) ... Counters:
Step #1 - "python_test":                                     test-file-rows =        100
Step #1 - "python_test":                          test-process_elapsed_time =       0.00
Step #1 - "python_test":                        test-process_remaining_time = 1000000.00
Step #1 - "python_test":                                     test-read-rows =          0
Step #1 - "python_test":                                    test-start_time =     257.28
Step #1 - "python_test": Counters:
Step #1 - "python_test":                                     test-file-rows =        100
Step #1 - "python_test":                          test-process_elapsed_time =       0.00
Step #1 - "python_test":                        test-process_remaining_time =       0.00
Step #1 - "python_test":                               test-processing_rate =   18272.88
Step #1 - "python_test":                                     test-read-rows =         10
Step #1 - "python_test":                                    test-start_time =     257.28
Step #1 - "python_test": ok
Step #1 - "python_test": test_dc_api_batched_wrapper (dc_api_wrapper_test.TestDCAPIWrapper.test_dc_api_batched_wrapper)
Step #1 - "python_test": Test DC API wrapper for batched calls. ... ok
Step #1 - "python_test": test_dc_api_is_defined_dcid (dc_api_wrapper_test.TestDCAPIWrapper.test_dc_api_is_defined_dcid)
Step #1 - "python_test": Test API wrapper for defined DCIDs. ... ok
Step #1 - "python_test": test_dc_api_wrapper (dc_api_wrapper_test.TestDCAPIWrapper.test_dc_api_wrapper)
Step #1 - "python_test": Test the wrapper for DC API. ... ok
Step #1 - "python_test": test_dc_get_node_property_values (dc_api_wrapper_test.TestDCAPIWrapper.test_dc_get_node_property_values)
Step #1 - "python_test": Test API wrapper to get all property:values for a node. ... ok
Step #1 - "python_test": test_download_file (download_util_test.TestCounters.test_download_file) ... ok
Step #1 - "python_test": test_prefilled_url (download_util_test.TestCounters.test_prefilled_url) ... ok
Step #1 - "python_test": test_request_url (download_util_test.TestCounters.test_request_url) ... ok
Step #1 - "python_test": test_read_write (file_util_test.FileIOTest.test_read_write) ... ok
Step #1 - "python_test": test_file_get_estimate_num_rows (file_util_test.FileUtilsTest.test_file_get_estimate_num_rows) ... ok
Step #1 - "python_test": test_file_get_matching (file_util_test.FileUtilsTest.test_file_get_matching) ... ok
Step #1 - "python_test": test_file_load_csv_dict (file_util_test.FileUtilsTest.test_file_load_csv_dict) ... ok
Step #1 - "python_test": test_file_type (file_util_test.FileUtilsTest.test_file_type) ... ok
Step #1 - "python_test": test_file_write_load_py_dict (file_util_test.FileUtilsTest.test_file_write_load_py_dict) ... ok
Step #1 - "python_test": test_aa2 (latlng2place_mapsapi_test.Latlng2PlaceMapsAPITest.test_aa2) ... ok
Step #1 - "python_test": test_country (latlng2place_mapsapi_test.Latlng2PlaceMapsAPITest.test_country) ... ok
Step #1 - "python_test": test_main (latlng_recon_geojson_test.LatlngReconGeojsonTest.test_main) ... ok
Step #1 - "python_test": test_basic (latlng_recon_service_test.LatlngReconServiceTest.test_basic) ... /usr/local/lib/python3.11/concurrent/futures/thread.py:58: ResourceWarning: unclosed <ssl.SSLSocket fd=3, family=2, type=1, proto=6, laddr=('192.168.10.3', 41254), raddr=('34.49.176.91', 443)>
Step #1 - "python_test":   result = self.fn(*self.args, **self.kwargs)
Step #1 - "python_test": ResourceWarning: Enable tracemalloc to get the object allocation traceback
Step #1 - "python_test": ok
Step #1 - "python_test": test_filter (latlng_recon_service_test.LatlngReconServiceTest.test_filter) ... /usr/local/lib/python3.11/concurrent/futures/thread.py:58: ResourceWarning: unclosed <ssl.SSLSocket fd=3, family=2, type=1, proto=6, laddr=('192.168.10.3', 41262), raddr=('34.49.176.91', 443)>
Step #1 - "python_test":   result = self.fn(*self.args, **self.kwargs)
Step #1 - "python_test": ResourceWarning: Enable tracemalloc to get the object allocation traceback
Step #1 - "python_test": ok
Step #1 - "python_test": test_dict_list_to_mcf_str (mcf_dict_util_test.TestMCFDict.test_dict_list_to_mcf_str) ... ok
Step #1 - "python_test": test_drop_nodes (mcf_dict_util_test.TestMCFDict.test_drop_nodes) ... ok
Step #1 - "python_test": test_get_dcid_node (mcf_dict_util_test.TestMCFDict.test_get_dcid_node) ... ok
Step #1 - "python_test": test_mcf_dict_rename_namespace (mcf_dict_util_test.TestMCFDict.test_mcf_dict_rename_namespace) ... ok
Step #1 - "python_test": test_mcf_dict_rename_prop (mcf_dict_util_test.TestMCFDict.test_mcf_dict_rename_prop) ... ok
Step #1 - "python_test": test_mcf_dict_rename_prop_value (mcf_dict_util_test.TestMCFDict.test_mcf_dict_rename_prop_value) ... ok
Step #1 - "python_test": test_mcf_to_dict_list (mcf_dict_util_test.TestMCFDict.test_mcf_to_dict_list) ... ok
Step #1 - "python_test": test_node_list_check_existence_dc (mcf_dict_util_test.TestMCFDict.test_node_list_check_existence_dc) ... ok
Step #1 - "python_test": test_node_list_check_existence_node_list (mcf_dict_util_test.TestMCFDict.test_node_list_check_existence_node_list) ... ok
Step #1 - "python_test": test_example_usage (mcf_template_filler_test.MCFTemplateFillerTest.test_example_usage) ... ok
Step #1 - "python_test": test_pop_and_2_obs_with_all_pv (mcf_template_filler_test.MCFTemplateFillerTest.test_pop_and_2_obs_with_all_pv)
Step #1 - "python_test": Use separate templates for Pop Obs, and use Obs template repeatedly. ... ok
Step #1 - "python_test": test_pop_with_missing_req_pv (mcf_template_filler_test.MCFTemplateFillerTest.test_pop_with_missing_req_pv) ... ok
Step #1 - "python_test": test_require_node_name (mcf_template_filler_test.MCFTemplateFillerTest.test_require_node_name) ... ok
Step #1 - "python_test": test_unified_pop_obs_with_missing_optional_pv (mcf_template_filler_test.MCFTemplateFillerTest.test_unified_pop_obs_with_missing_optional_pv) ... ok
Step #1 - "python_test": test_place_id_resolution_by_name (state_division_to_dcid_test.PlaceMapTest.test_place_id_resolution_by_name) ... ok
Step #1 - "python_test": test_boolean_naming (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_boolean_naming) ... ok
Step #1 - "python_test": test_double_underscore (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_double_underscore) ... ok
Step #1 - "python_test": test_ignore_props (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_ignore_props) ... ok
Step #1 - "python_test": test_legacy_mapping (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_legacy_mapping) ... ok
Step #1 - "python_test": test_measured_property (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_measured_property) ... ok
Step #1 - "python_test": test_measurement_constraint_removal (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_measurement_constraint_removal) ... ok
Step #1 - "python_test": test_measurement_denominator (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_measurement_denominator) ... ok
Step #1 - "python_test": test_measurement_qualifier (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_measurement_qualifier) ... ok
Step #1 - "python_test": test_naics_name_generation (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_naics_name_generation) ... ok
Step #1 - "python_test": test_namespace_removal (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_namespace_removal) ... ok
Step #1 - "python_test": test_prepend_append_replace (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_prepend_append_replace) ... ok
Step #1 - "python_test": test_quantity_name_generation (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_quantity_name_generation) ... ok
Step #1 - "python_test": test_quantity_range_name_generation (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_quantity_range_name_generation) ... ok
Step #1 - "python_test": test_soc_map (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_soc_map) ... ok
Step #1 - "python_test": test_soc_name_generation (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_soc_name_generation) ... ok
Step #1 - "python_test": test_sorted_constraints (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_sorted_constraints) ... ok
Step #1 - "python_test": test_stat_type (statvar_dcid_generator_test.TestStatVarDcidGenerator.test_stat_type) ... ok
Step #1 - "python_test": 
Step #1 - "python_test": ----------------------------------------------------------------------
Step #1 - "python_test": Ran 61 tests in 4.044s
Step #1 - "python_test": 
Step #1 - "python_test": OK
Step #1 - "python_test": ### Running Python tests in import-automation/executor
Step #2 - "python_format_check": --- scripts/biomedical/diseasesAtJensenLab/scripts/format_disease_jensen_lab.py	(original)
Step #2 - "python_format_check": +++ scripts/biomedical/diseasesAtJensenLab/scripts/format_disease_jensen_lab.py	(reformatted)
Step #2 - "python_format_check": @@ -30,68 +30,74 @@
Step #2 - "python_format_check":  import pandas as pd
Step #2 - "python_format_check":  import time
Step #2 - "python_format_check":  
Step #2 - "python_format_check": -
Step #2 - "python_format_check":  # declare universal variables
Step #2 - "python_format_check": -HGNC_DICT = {'HGNC:9982':'RFX1', 'HGNC:9979':'RFPL2'}
Step #2 - "python_format_check": +HGNC_DICT = {'HGNC:9982': 'RFX1', 'HGNC:9979': 'RFPL2'}
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  def filter_for_lowest_ICD10_level(df):
Step #2 - "python_format_check": -	# initiate values
Step #2 - "python_format_check": -	indices_to_drop = []
Step #2 - "python_format_check": -	previous_ICD10 = ''
Step #2 - "python_format_check": -	previous_gene = ''
Step #2 - "python_format_check": -	previous_index = -1
Step #2 - "python_format_check": -	# check if ICD10 code is more specific than previous row for the same gene
Step #2 - "python_format_check": -	# if it is add the previous ICD10 code index to the list of indices to drop
Step #2 - "python_format_check": -	for index, row in df.iterrows():
Step #2 - "python_format_check": -		current_ICD10 = row['ICD10']
Step #2 - "python_format_check": -		current_gene = row['Gene']
Step #2 - "python_format_check": -		if current_gene == previous_gene and current_ICD10.startswith(previous_ICD10):
Step #2 - "python_format_check": -			indices_to_drop.append(previous_index)
Step #2 - "python_format_check": -		# update reference values
Step #2 - "python_format_check": -		previous_ICD10 = current_ICD10
Step #2 - "python_format_check": -		previous_gene = current_gene
Step #2 - "python_format_check": -		previous_index = index
Step #2 - "python_format_check": -	# drop rows with less specific ICD10 codes for a given gene
Step #2 - "python_format_check": -	df.drop(indices_to_drop, axis=0, inplace=True)
Step #2 - "python_format_check": -	return df
Step #2 - "python_format_check": +    # initiate values
Step #2 - "python_format_check": +    indices_to_drop = []
Step #2 - "python_format_check": +    previous_ICD10 = ''
Step #2 - "python_format_check": +    previous_gene = ''
Step #2 - "python_format_check": +    previous_index = -1
Step #2 - "python_format_check": +    # check if ICD10 code is more specific than previous row for the same gene
Step #2 - "python_format_check": +    # if it is add the previous ICD10 code index to the list of indices to drop
Step #2 - "python_format_check": +    for index, row in df.iterrows():
Step #2 - "python_format_check": +        current_ICD10 = row['ICD10']
Step #2 - "python_format_check": +        current_gene = row['Gene']
Step #2 - "python_format_check": +        if current_gene == previous_gene and current_ICD10.startswith(
Step #2 - "python_format_check": +                previous_ICD10):
Step #2 - "python_format_check": +            indices_to_drop.append(previous_index)
Step #2 - "python_format_check": +        # update reference values
Step #2 - "python_format_check": +        previous_ICD10 = current_ICD10
Step #2 - "python_format_check": +        previous_gene = current_gene
Step #2 - "python_format_check": +        previous_index = index
Step #2 - "python_format_check": +    # drop rows with less specific ICD10 codes for a given gene
Step #2 - "python_format_check": +    df.drop(indices_to_drop, axis=0, inplace=True)
Step #2 - "python_format_check": +    return df
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  def fix_ICD10_formatting(df, col):
Step #2 - "python_format_check": -	# if string in specified column is 10 characters or longer
Step #2 - "python_format_check": -	# add '.' in the 10th position
Step #2 - "python_format_check": +    # if string in specified column is 10 characters or longer
Step #2 - "python_format_check": +    # add '.' in the 10th position
Step #2 - "python_format_check":      mask = df[col].str.len() >= 10
Step #2 - "python_format_check": -    df.loc[mask, col] = df.loc[mask, col].str[:9] + '.' + df.loc[mask, col].str[9:]
Step #2 - "python_format_check": +    df.loc[mask,
Step #2 - "python_format_check": +           col] = df.loc[mask, col].str[:9] + '.' + df.loc[mask, col].str[9:]
Step #2 - "python_format_check":      return df
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  def format_icd10_code_dcids(df):
Step #2 - "python_format_check": -	df_doid = df.dropna(subset=['DOID'])  # make a doid specific table
Step #2 - "python_format_check": -	## filter out ICD-10 codes based on true existence - remove codes like C1, C2 and root
Step #2 - "python_format_check": -	df['count'] = np.where(df['ICD10'] == df['ICD10'],df['ICD10'].str.split(':'),np.nan)
Step #2 - "python_format_check": -	df['count'] = np.where(df['count'] == df['count'],df['count'].str[1],np.nan)
Step #2 - "python_format_check": -	# remove non-existing ICD-10 codes
Step #2 - "python_format_check": -	df = df[df['count']!='root']
Step #2 - "python_format_check": -	df.loc[:, 'count'] = df['count'].str.len()
Step #2 - "python_format_check": -	df = df[df['count'] > 2]
Step #2 - "python_format_check": -	df = filter_for_lowest_ICD10_level(df)
Step #2 - "python_format_check": -	# fix ill formatted ICD10 codes
Step #2 - "python_format_check": -	df = fix_ICD10_formatting(df, 'Disease')
Step #2 - "python_format_check": -	df = fix_ICD10_formatting(df, 'Disease_Name')
Step #2 - "python_format_check": -	df = fix_ICD10_formatting(df, 'ICD10')
Step #2 - "python_format_check": -	# join back with the doid rows
Step #2 - "python_format_check": -	df_final = pd.concat([df, df_doid]).sort_index()
Step #2 - "python_format_check": -	return df_final
Step #2 - "python_format_check": +    df_doid = df.dropna(subset=['DOID'])  # make a doid specific table
Step #2 - "python_format_check": +    ## filter out ICD-10 codes based on true existence - remove codes like C1, C2 and root
Step #2 - "python_format_check": +    df['count'] = np.where(df['ICD10'] == df['ICD10'],
Step #2 - "python_format_check": +                           df['ICD10'].str.split(':'), np.nan)
Step #2 - "python_format_check": +    df['count'] = np.where(df['count'] == df['count'], df['count'].str[1],
Step #2 - "python_format_check": +                           np.nan)
Step #2 - "python_format_check": +    # remove non-existing ICD-10 codes
Step #2 - "python_format_check": +    df = df[df['count'] != 'root']
Step #2 - "python_format_check": +    df.loc[:, 'count'] = df['count'].str.len()
Step #2 - "python_format_check": +    df = df[df['count'] > 2]
Step #2 - "python_format_check": +    df = filter_for_lowest_ICD10_level(df)
Step #2 - "python_format_check": +    # fix ill formatted ICD10 codes
Step #2 - "python_format_check": +    df = fix_ICD10_formatting(df, 'Disease')
Step #2 - "python_format_check": +    df = fix_ICD10_formatting(df, 'Disease_Name')
Step #2 - "python_format_check": +    df = fix_ICD10_formatting(df, 'ICD10')
Step #2 - "python_format_check": +    # join back with the doid rows
Step #2 - "python_format_check": +    df_final = pd.concat([df, df_doid]).sort_index()
Step #2 - "python_format_check": +    return df_final
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  def format_doid_icd(df):
Step #2 - "python_format_check": -	df['DOID'] = np.where(df['Disease'].str.contains('DOID'),df['Disease'],np.nan)
Step #2 - "python_format_check": -	df['ICD10'] = np.where(df['Disease'].str.contains('ICD10'),df['Disease'],np.nan)
Step #2 - "python_format_check": -	## identify ensemblIDs and set as new column
Step #2 - "python_format_check": -	df['ensemblID'] = np.where(df['Id'].str.contains('ENSP00000'),df['Id'],np.nan)
Step #2 - "python_format_check": -	## format icd10 dcids filtering for the most specific ICD10 code
Step #2 - "python_format_check": -	df = format_icd10_code_dcids(df)
Step #2 - "python_format_check": -	return df
Step #2 - "python_format_check": +    df['DOID'] = np.where(df['Disease'].str.contains('DOID'), df['Disease'],
Step #2 - "python_format_check": +                          np.nan)
Step #2 - "python_format_check": +    df['ICD10'] = np.where(df['Disease'].str.contains('ICD10'), df['Disease'],
Step #2 - "python_format_check": +                           np.nan)
Step #2 - "python_format_check": +    ## identify ensemblIDs and set as new column
Step #2 - "python_format_check": +    df['ensemblID'] = np.where(df['Id'].str.contains('ENSP00000'), df['Id'],
Step #2 - "python_format_check": +                               np.nan)
Step #2 - "python_format_check": +    ## format icd10 dcids filtering for the most specific ICD10 code
Step #2 - "python_format_check": +    df = format_icd10_code_dcids(df)
Step #2 - "python_format_check": +    return df
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  def check_for_illegal_charc(s):
Step #2 - "python_format_check": @@ -100,7 +106,9 @@
Step #2 - "python_format_check":          s: target string that needs to be checked
Step #2 - "python_format_check":      
Step #2 - "python_format_check":      """
Step #2 - "python_format_check": -    list_illegal = ["'", "*" ">", "<", "@", "]", "[", "|", ":", ";" " "]
Step #2 - "python_format_check": +    list_illegal = ["'", "*"
Step #2 - "python_format_check": +                    ">", "<", "@", "]", "[", "|", ":", ";"
Step #2 - "python_format_check": +                    " "]
Step #2 - "python_format_check":      if any([x in s for x in list_illegal]):
Step #2 - "python_format_check":          print('Error! dcid contains illegal characters!', s)
Step #2 - "python_format_check":  
Step #2 - "python_format_check": @@ -114,7 +122,7 @@
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  def format_disease_gene_cols(df, data_type):
Step #2 - "python_format_check": -	# handle exceptions in Gene names
Step #2 - "python_format_check": +    # handle exceptions in Gene names
Step #2 - "python_format_check":      df['Gene'] = df['Gene'].map(HGNC_DICT).fillna(df['Gene'])
Step #2 - "python_format_check":      df['Gene'] = df['Gene'].str.replace('@', '_Cluster')
Step #2 - "python_format_check":      # generate gene dcid
Step #2 - "python_format_check": @@ -129,122 +137,148 @@
Step #2 - "python_format_check":      df['Disease_dcid'] = df['Disease_dcid'].fillna(df['ICD10_dcid'])
Step #2 - "python_format_check":      df['Disease_dcid'] = 'dcid:' + df['Disease_dcid']
Step #2 - "python_format_check":      # generate dcid for DiseaseGeneAssociation nodes
Step #2 - "python_format_check": -    df['dcid'] = 'bio/' + df['Disease'].astype(str).str.replace(':', '_', regex=False) + '_' + df['Gene'].astype(str) + '_association'
Step #2 - "python_format_check": +    df['dcid'] = 'bio/' + df['Disease'].astype(str).str.replace(
Step #2 - "python_format_check": +        ':', '_', regex=False) + '_' + df['Gene'].astype(str) + '_association'
Step #2 - "python_format_check":      # format name for DiseaseGeneAssociation nodes
Step #2 - "python_format_check": -    df['name'] = df['Disease_Name'].astype(str) + ' and ' + df['Gene'].astype(str) + ' association'
Step #2 - "python_format_check": +    df['name'] = df['Disease_Name'].astype(str) + ' and ' + df['Gene'].astype(
Step #2 - "python_format_check": +        str) + ' association'
Step #2 - "python_format_check":      # drop columns not used in import
Step #2 - "python_format_check":      df = df.drop(['Disease'], axis=1)
Step #2 - "python_format_check":      return df
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  
Step #2 - "python_format_check":  def format_RNA_type(df_tm):
Step #2 - "python_format_check": -	gene_list = ['orf', 'ZNF']
Step #2 - "python_format_check": -	sno_rna_list = ['sno', 'SNOR', 'SCAR']
Step #2 - "python_format_check": -	linc_rna_list = ['LINC', 'linc', 'MIR']
Step #2 - "python_format_check": -	df_tm['RNA_type'] = 'dcs:NonCodingRNATypeLongNonCodingRNA'
Step #2 - "python_format_check": -	df_tm['RNA_type'] = np.where(df_tm["Gene"].str.contains('|'.join(gene_list)),'Gene', df_tm['RNA_type'])
Step #2 - "python_format_check": -	df_tm['RNA_type'] = np.where(
...
[Logs truncated due to log size limitations. For full logs, see https://console.cloud.google.com/cloud-build/builds/d83f5c9f-9607-474e-b9f5-11a721914ec4?project=879489846695.]
...
": -    main() 
Step #2 - "python_format_check": -    
Step #2 - "python_format_check": +    main()
Step #1 - "python_test": Installing Python requirements
Step #1 - "python_test": 
Step #1 - "python_test": [notice] A new release of pip is available: 24.0 -> 24.3.1
Step #1 - "python_test": [notice] To update, run: pip install --upgrade pip
Step #1 - "python_test": #### Testing Python code in import-automation/executor
Step #1 - "python_test": test_appengine_job_request (test.cloud_scheduler_test.CloudSchedulerTest.test_appengine_job_request) ... ok
Step #1 - "python_test": test_http_job_request (test.cloud_scheduler_test.CloudSchedulerTest.test_http_job_request) ... ok
Step #1 - "python_test": test.file_uploader_test (unittest.loader._FailedTest.test.file_uploader_test) ... ERROR
Step #1 - "python_test": test.github_api_test (unittest.loader._FailedTest.test.github_api_test) ... ERROR
Step #1 - "python_test": test_clean_time (test.import_executor_test.ImportExecutorTest.test_clean_time) ... ok
Step #1 - "python_test": test_construct_process_message (test.import_executor_test.ImportExecutorTest.test_construct_process_message) ... ok
Step #1 - "python_test": test_construct_process_message_no_output (test.import_executor_test.ImportExecutorTest.test_construct_process_message_no_output)
Step #1 - "python_test": Tests that _construct_process_message does not append ... ok
Step #1 - "python_test": test_create_venv (test.import_executor_test.ImportExecutorTest.test_create_venv) ... ok
Step #1 - "python_test": test_run_and_handle_exception (test.import_executor_test.ImportExecutorTest.test_run_and_handle_exception) ... ERROR:root:An unexpected exception was thrown
Step #1 - "python_test": Traceback (most recent call last):
Step #1 - "python_test":   File "/workspace/import-automation/executor/app/executor/import_executor.py", line 489, in run_and_handle_exception
Step #1 - "python_test":     return exec_func(*args)
Step #1 - "python_test":            ^^^^^^^^^^^^^^^^
Step #1 - "python_test": TypeError: 'str' object is not callable
Step #1 - "python_test": FAIL
Step #1 - "python_test": test_run_with_timeout (test.import_executor_test.ImportExecutorTest.test_run_with_timeout) ... ERROR:root:An unexpected exception was thrown: Command '['sleep', '5']' timed out after 0.1 seconds when running ['sleep', '5']: Traceback (most recent call last):
Step #1 - "python_test":   File "/workspace/import-automation/executor/app/executor/import_executor.py", line 588, in _run_with_timeout
Step #1 - "python_test":     process = subprocess.run(args,
Step #1 - "python_test":               ^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 550, in run
Step #1 - "python_test":     stdout, stderr = process.communicate(input, timeout=timeout)
Step #1 - "python_test":                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 1209, in communicate
Step #1 - "python_test":     stdout, stderr = self._communicate(input, endtime, timeout)
Step #1 - "python_test":                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 2116, in _communicate
Step #1 - "python_test":     self._check_timeout(endtime, orig_timeout, stdout, stderr)
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 1253, in _check_timeout
Step #1 - "python_test":     raise TimeoutExpired(
Step #1 - "python_test": subprocess.TimeoutExpired: Command '['sleep', '5']' timed out after 0.1 seconds
Step #1 - "python_test": Traceback (most recent call last):
Step #1 - "python_test":   File "/workspace/import-automation/executor/app/executor/import_executor.py", line 588, in _run_with_timeout
Step #1 - "python_test":     process = subprocess.run(args,
Step #1 - "python_test":               ^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 550, in run
Step #1 - "python_test":     stdout, stderr = process.communicate(input, timeout=timeout)
Step #1 - "python_test":                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 1209, in communicate
Step #1 - "python_test":     stdout, stderr = self._communicate(input, endtime, timeout)
Step #1 - "python_test":                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 2116, in _communicate
Step #1 - "python_test":     self._check_timeout(endtime, orig_timeout, stdout, stderr)
Step #1 - "python_test":   File "/usr/local/lib/python3.11/subprocess.py", line 1253, in _check_timeout
Step #1 - "python_test":     raise TimeoutExpired(
Step #1 - "python_test": subprocess.TimeoutExpired: Command '['sleep', '5']' timed out after 0.1 seconds
Step #1 - "python_test": FAIL
Step #1 - "python_test": test_are_imports_finished (test.import_service_test.ImportServiceTest.test_are_imports_finished) ... ok
Step #1 - "python_test": test_block_on_import (test.import_service_test.ImportServiceTest.test_block_on_import) ... ok
Step #1 - "python_test": test_fix_input_path (test.import_service_test.ImportServiceTest.test_fix_input_path) ... ok
Step #1 - "python_test": test_format_import_info (test.import_service_test.ImportServiceTest.test_format_import_info) ... ok
Step #1 - "python_test": test_get_fixed_absolute_import_name (test.import_service_test.ImportServiceTest.test_get_fixed_absolute_import_name) ... ok
Step #1 - "python_test": test_get_import_id (test.import_service_test.ImportServiceTest.test_get_import_id) ... ok
Step #1 - "python_test": test_smart_import (test.import_service_test.ImportServiceTest.test_smart_import) ... ok
Step #1 - "python_test": test_absolute_import_name (test.import_target_test.ImportTargetTest.test_absolute_import_name) ... ok
Step #1 - "python_test": test_is_import_targetted_by_commit (test.import_target_test.ImportTargetTest.test_is_import_targetted_by_commit) ... ok
Step #1 - "python_test": test_parse_commit_message_targets (test.import_target_test.ImportTargetTest.test_parse_commit_message_targets) ... ok
Step #1 - "python_test": test.integration_test (unittest.loader._FailedTest.test.integration_test) ... ERROR
Step #1 - "python_test": test_download_file (test.utils_test.AppUtilsTest.test_download_file)
Step #1 - "python_test": Response does not have a Content-Disposition header. ... ok
Step #1 - "python_test": test_download_file_timeout (test.utils_test.AppUtilsTest.test_download_file_timeout)
Step #1 - "python_test": Raises requests.Timeout exception. ... ok
Step #1 - "python_test": test_get_filename (test.utils_test.AppUtilsTest.test_get_filename) ... ok
Step #1 - "python_test": test_get_filename_raise (test.utils_test.AppUtilsTest.test_get_filename_raise) ... ok
Step #1 - "python_test": test_pacific_time_to_datetime (test.utils_test.AppUtilsTest.test_pacific_time_to_datetime)
Step #1 - "python_test": Tests that the string returned by pacific_time can be converted to ... ok
Step #1 - "python_test": test_pacific_time_to_datetime_then_back (test.utils_test.AppUtilsTest.test_pacific_time_to_datetime_then_back)
Step #1 - "python_test": Tests that the string returned by pacific_time can be converted to ... ok
Step #1 - "python_test": test_compare_lines (test.utils_test.TestUtilsTest.test_compare_lines) ... ok
Step #1 - "python_test": test_import_spec_valid (test.validation_test.ValidationTest.test_import_spec_valid) ... ok
Step #1 - "python_test": test_import_spec_valid_fields_absent (test.validation_test.ValidationTest.test_import_spec_valid_fields_absent) ... ok
Step #1 - "python_test": test_import_spec_valid_script_not_exist (test.validation_test.ValidationTest.test_import_spec_valid_script_not_exist) ... ok
Step #1 - "python_test": test_import_targets_valid_absolute_names (test.validation_test.ValidationTest.test_import_targets_valid_absolute_names) ... ok
Step #1 - "python_test": test_import_targets_valid_manifest_not_exist (test.validation_test.ValidationTest.test_import_targets_valid_manifest_not_exist) ... ok
Step #1 - "python_test": test_import_targets_valid_name_not_exist (test.validation_test.ValidationTest.test_import_targets_valid_name_not_exist) ... ok
Step #1 - "python_test": test_import_targets_valid_relative_names (test.validation_test.ValidationTest.test_import_targets_valid_relative_names) ... ok
Step #1 - "python_test": test_import_targets_valid_relative_names_multiple_dirs (test.validation_test.ValidationTest.test_import_targets_valid_relative_names_multiple_dirs) ... ok
Step #1 - "python_test": test_manifest_valid_fields_absent (test.validation_test.ValidationTest.test_manifest_valid_fields_absent) ... ok
Step #1 - "python_test": 
Step #1 - "python_test": ======================================================================
Step #1 - "python_test": ERROR: test.file_uploader_test (unittest.loader._FailedTest.test.file_uploader_test)
Step #1 - "python_test": ----------------------------------------------------------------------
Step #1 - "python_test": ImportError: Failed to import test module: test.file_uploader_test
Step #1 - "python_test": Traceback (most recent call last):
Step #1 - "python_test":   File "/usr/local/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
Step #1 - "python_test":     module = self._get_module_from_name(name)
Step #1 - "python_test":              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
Step #1 - "python_test":     __import__(name)
Step #1 - "python_test":   File "/workspace/import-automation/executor/test/file_uploader_test.py", line 22, in <module>
Step #1 - "python_test":     from test import integration_test
Step #1 - "python_test":   File "/workspace/import-automation/executor/test/integration_test.py", line 30, in <module>
Step #1 - "python_test":     'github_repo_owner_username': os.environ['_GITHUB_REPO_OWNER_USERNAME'],
Step #1 - "python_test":                                   ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "<frozen os>", line 679, in __getitem__
Step #1 - "python_test": KeyError: '_GITHUB_REPO_OWNER_USERNAME'
Step #1 - "python_test": 
Step #1 - "python_test": 
Step #1 - "python_test": ======================================================================
Step #1 - "python_test": ERROR: test.github_api_test (unittest.loader._FailedTest.test.github_api_test)
Step #1 - "python_test": ----------------------------------------------------------------------
Step #1 - "python_test": ImportError: Failed to import test module: test.github_api_test
Step #1 - "python_test": Traceback (most recent call last):
Step #1 - "python_test":   File "/usr/local/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
Step #1 - "python_test":     module = self._get_module_from_name(name)
Step #1 - "python_test":              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
Step #1 - "python_test":     __import__(name)
Step #1 - "python_test":   File "/workspace/import-automation/executor/test/github_api_test.py", line 28, in <module>
Step #1 - "python_test":     from test import integration_test
Step #1 - "python_test":   File "/workspace/import-automation/executor/test/integration_test.py", line 30, in <module>
Step #1 - "python_test":     'github_repo_owner_username': os.environ['_GITHUB_REPO_OWNER_USERNAME'],
Step #1 - "python_test":                                   ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "<frozen os>", line 679, in __getitem__
Step #1 - "python_test": KeyError: '_GITHUB_REPO_OWNER_USERNAME'
Step #1 - "python_test": 
Step #1 - "python_test": 
Step #1 - "python_test": ======================================================================
Step #1 - "python_test": ERROR: test.integration_test (unittest.loader._FailedTest.test.integration_test)
Step #1 - "python_test": ----------------------------------------------------------------------
Step #1 - "python_test": ImportError: Failed to import test module: test.integration_test
Step #1 - "python_test": Traceback (most recent call last):
Step #1 - "python_test":   File "/usr/local/lib/python3.11/unittest/loader.py", line 419, in _find_test_path
Step #1 - "python_test":     module = self._get_module_from_name(name)
Step #1 - "python_test":              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/usr/local/lib/python3.11/unittest/loader.py", line 362, in _get_module_from_name
Step #1 - "python_test":     __import__(name)
Step #1 - "python_test":   File "/workspace/import-automation/executor/test/integration_test.py", line 30, in <module>
Step #1 - "python_test":     'github_repo_owner_username': os.environ['_GITHUB_REPO_OWNER_USERNAME'],
Step #1 - "python_test":                                   ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "<frozen os>", line 679, in __getitem__
Step #1 - "python_test": KeyError: '_GITHUB_REPO_OWNER_USERNAME'
Step #1 - "python_test": 
Step #1 - "python_test": 
Step #1 - "python_test": ======================================================================
Step #1 - "python_test": FAIL: test_run_and_handle_exception (test.import_executor_test.ImportExecutorTest.test_run_and_handle_exception)
Step #1 - "python_test": ----------------------------------------------------------------------
Step #1 - "python_test": Traceback (most recent call last):
Step #1 - "python_test":   File "/usr/local/lib/python3.11/unittest/mock.py", line 1378, in patched
Step #1 - "python_test":     return func(*newargs, **newkeywargs)
Step #1 - "python_test":            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Step #1 - "python_test":   File "/workspace/import-automation/executor/test/import_executor_test.py", line 69, in test_run_and_handle_exception
Step #1 - "python_test":     self.assertIn('Exception', result.message)
Step #1 - "python_test": AssertionError: 'Exception' not found in 'Traceback (most recent call last):\n  File "/workspace/import-automation/executor/app/executor/import_executor.py", line 489, in run_and_handle_exception\n    return exec_func(*args)\n           ^^^^^^^^^^^^^^^^\nTypeError: \'str\' object is not callable\n'
Step #1 - "python_test": 
Step #1 - "python_test": ======================================================================
Step #1 - "python_test": FAIL: test_run_with_timeout (test.import_executor_test.ImportExecutorTest.test_run_with_timeout)
Step #1 - "python_test": ----------------------------------------------------------------------
Step #1 - "python_test": Traceback (most recent call last):
Step #1 - "python_test":   File "/workspace/import-automation/executor/test/import_executor_test.py", line 37, in test_run_with_timeout
Step #1 - "python_test":     self.assertRaises(subprocess.TimeoutExpired,
Step #1 - "python_test": AssertionError: TimeoutExpired not raised by _run_with_timeout
Step #1 - "python_test": 
Step #1 - "python_test": ----------------------------------------------------------------------
Step #1 - "python_test": Ran 37 tests in 12.810s
Step #1 - "python_test": 
Step #1 - "python_test": FAILED (failures=2, errors=3)
Step #1 - "python_test": ### Running Python tests in scripts/
Step #1 - "python_test": Installing Python requirements
Step #1 - "python_test": 
Step #1 - "python_test": [notice] A new release of pip is available: 24.0 -> 24.3.1
Step #1 - "python_test": [notice] To update, run: pip install --upgrade pip
Step #1 - "python_test": #### Testing Python code in scripts/
Step #1 - "python_test": test_write_csv (aqicn.aqicn_test.AqicnTest.test_write_csv) ... ok
Step #1 - "python_test": test_main (biomedical.antibodyABCD.parse_abcd_test.TestParseAbcd.test_main)
Step #1 - "python_test": Test in the main function ... ok
Step #1 - "python_test": test_MergeAndProcessData (climate_trace.preprocess_data_test.PreprocessDataTest.test_MergeAndProcessData) ... ok
Step #1 - "python_test": test_create_csv (covid19_india.cases_count_states_data.preprocess_test.TestPreprocessCSVTest.test_create_csv) ... ok
Step #1 - "python_test": test_create_csv_include_dn_dd (covid19_india.cases_count_states_data.preprocess_test.TestPreprocessCSVTest.test_create_csv_include_dn_dd) ... ok
Step #1 - "python_test": test_create_csv_ingore_invalid_state (covid19_india.cases_count_states_data.preprocess_test.TestPreprocessCSVTest.test_create_csv_ingore_invalid_state) ... ok
Step #1 - "python_test": test_create_csv_latest_report_of_the_day (covid19_india.cases_count_states_data.preprocess_test.TestPreprocessCSVTest.test_create_csv_latest_report_of_the_day) ... ok
Step #1 - "python_test": test_create_csv_skip_unassigned (covid19_india.cases_count_states_data.preprocess_test.TestPreprocessCSVTest.test_create_csv_skip_unassigned) ... ok
Step #1 - "python_test": test_create_csv (covid19_india.medical_tests_in_data.preprocess_test.TestPreprocessCSVTest.test_create_csv) ... ok
Step #1 - "python_test": test_create_csv_remove_duplicate_dates (covid19_india.medical_tests_in_data.preprocess_test.TestPreprocessCSVTest.test_create_csv_remove_duplicate_dates) ... ok
Step #1 - "python_test": test_generate_tmcf (covid_tracking_project.historic_state_data.preprocess_csv_test.TestPreprocessCSVTest.test_generate_tmcf) ... ok
Step #1 - "python_test": test_write_csv (deepsolar.deepsolar_test.TestDeepSolar.test_write_csv) ... ok
Step #1 - "python_test": test_geocode_city (fbi.crime.geocode_cities_test.GeocodeCitiesTest.test_geocode_city) ... ok
Step #1 - "python_test": test_manual_geocode_city (fbi.crime.geocode_cities_test.GeocodeCitiesTest.test_manual_geocode_city) ... ok
Step #1 - "python_test": test_update_crime_geocode (fbi.crime.geocode_cities_test.GeocodeCitiesTest.test_update_crime_geocode) ... ok
Step #1 - "python_test": test_calculate_crimes (fbi.crime.preprocess_states_test.CleanCrimeFileTest.test_calculate_crimes) ... ok
Step #1 - "python_test": test_clean_crime_file (fbi.crime.preprocess_states_test.CleanCrimeFileTest.test_clean_crime_file) ... ok
Step #1 - "python_test": test_create_tmcf (fbi.crime.preprocess_states_test.CleanCrimeFileTest.test_create_tmcf) ... ok
Step #1 - "python_test": test_calculate_crimes (fbi.crime.preprocess_test.CleanCrimeFileTest.test_calculate_crimes) ... ok
Step #1 - "python_test": test_clean_crime_file (fbi.crime.preprocess_test.CleanCrimeFileTest.test_clean_crime_file) ... ok
Step #1 - "python_test": test_create_tmcf (fbi.crime.preprocess_test.CleanCrimeFileTest.test_create_tmcf) ... ok
Step #1 - "python_test": test_extract_geojsons (fires.perimeter.wfigs_fire_perimeter_test.PerimeterDataTest.test_extract_geojsons) ... ok
Step #1 - "python_test": test_ProcessDF (fires.wfigs_data_test.PreprocessDataTest.test_ProcessDF) ... /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": /workspace/scripts/fires/wfigs_data_test.py:43: FutureWarning: Mismatched null-like values None and nan found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise.
Step #1 - "python_test":   pd.testing.assert_frame_equal(processed,
Step #1 - "python_test": ok
Step #1 - "python_test": test1 (google_datasets.covid_mobility.covidmobility_test.TestCovidMobility.test1)
Step #1 - "python_test": Simple test 1 ... ok
Step #1 - "python_test": test2 (google_datasets.covid_mobility.covidmobility_test.TestCovidMobility.test2)
Step #1 - "python_test": Simple test 2 ... ok
Step #1 - "python_test": test3 (google_datasets.covid_mobility.covidmobility_test.TestCovidMobility.test3)
Step #1 - "python_test": Tests a row with empty data. ... ok
Step #1 - "python_test": test4 (google_datasets.covid_mobility.covidmobility_test.TestCovidMobility.test4)
Step #1 - "python_test": Tests a row with an empty date. ... ok
Step #1 - "python_test": test_format_census2001_district_code (india.formatters_test.TestPreprocess.test_format_census2001_district_code) ... ok
Step #1 - "python_test": test_format_census2011_code (india.formatters_test.TestPreprocess.test_format_census2011_code) ... ok
Step #1 - "python_test": test_format_lgd_district_code (india.formatters_test.TestPreprocess.test_format_lgd_district_code) ... ok
Step #1 - "python_test": test_format_lgd_state_code (india.formatters_test.TestPreprocess.test_format_lgd_state_code) ... ok
Step #1 - "python_test": test_get_district_name_to_lgd_code_mapping (india.geo.districts_test.TestPreprocess.test_get_district_name_to_lgd_code_mapping) ... ok
Step #1 - "python_test": test_get_state_name_to_census2001_code_mapping (india.geo.states_test.TestPreprocess.test_get_state_name_to_census2001_code_mapping) ... ok
Step #1 - "python_test": test_get_state_name_to_iso_code_mapping (india.geo.states_test.TestPreprocess.test_get_state_name_to_iso_code_mapping) ... ok
Step #1 - "python_test": test_create_csv (india_aqi.preprocess_test.TestPreprocess.test_create_csv) ... /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": /workspace/scripts/india_aqi/preprocess.py:89: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
Step #1 - "python_test":   self.clean_df[column] = pd.to_numeric(self.clean_df[column],
Step #1 - "python_test": ok
Step #1 - "python_test": test_create_csv (india_census.common.base_test.TestCensusPrimaryAbstractDataLoaderBase.test_create_csv) ... ok
Step #2 - "python_format_check": ERROR: Fix lint errors by running ./run_tests.sh -f
Finished Step #2 - "python_format_check"
ERROR
ERROR: build step 2 "python:3.11" failed: step exited with non-zero status: 1
Step #1 - "python_test": test_create_csv_literate_data (india_census.common.base_test.TestCensusPrimaryAbstractDataLoaderBase.test_create_csv_literate_data) ...