Sourcery refactored master branch #39
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| pubmed_info[pmid] = {} | ||
| pubmed_info[pmid]['title'] = article['title'] | ||
| pubmed_info[pmid]['journal'] = article['journal'] | ||
| pubmed_info[pmid]['year'] = article['year'] | ||
| pubmed_info[pmid]['author'] = article['authors'][0] | ||
| pubmed_info[pmid] = { | ||
| 'title': article['title'], | ||
| 'journal': article['journal'], | ||
| 'year': article['year'], | ||
| 'author': article['authors'][0], | ||
| } | ||
| except Exception: | ||
| for pubmed_id in litvar_data[0]['pmids']: | ||
| pmid = int(pubmed_id) | ||
| pubmed_info[pmid] = {} | ||
| pubmed_info[pmid]['title'] = '' | ||
| pubmed_info[pmid] = {'title': ''} |
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Function litvar refactored with the following changes:
- Merge dictionary assignment with declaration [×5] (
merge-dict-assign)
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| match_rsid = re.search(r'^(rs\d+)$', request.form['rsid']) | ||
| if match_rsid: | ||
| rsid = match_rsid.group(1) | ||
| if match_rsid := re.search(r'^(rs\d+)$', request.form['rsid']): | ||
| rsid = match_rsid[1] |
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Function litvar2 refactored with the following changes:
- Use named expression to simplify assignment and conditional (
use-named-expression) - Replace m.group(x) with m[x] for re.Match objects (
use-getitem-for-re-match-groups) - Merge dictionary assignment with declaration [×6] (
merge-dict-assign)
| variant_id = match_varid.group(1) | ||
| variant_id = match_varid[1] | ||
| # genome = request.form['genome'] | ||
| genome = match_genome.group(1) | ||
| genome = match_genome[1] |
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Function defgen refactored with the following changes:
- Replace m.group(x) with m[x] for re.Match objects [×2] (
use-getitem-for-re-match-groups) - Move setting of default value for variable into
elsebranch (introduce-default-else) - Replace call to format with f-string (
use-fstring-for-formatting) - Move assignment closer to its usage within a block (
move-assign-in-block) - Replace if statement with if expression (
assign-if-exp) - Replace assignment and augmented assignment with single assignment (
merge-assign-and-aug-assign)
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| genome = match_genome.group(1) | ||
| chrom = match_nochr_chrom.group(1) | ||
| pos = match_pos.group(1) | ||
| ref = match_ref.group(1) | ||
| alt = match_alt.group(1) | ||
| gene = match_gene_symbol.group(1) | ||
| genome = match_genome[1] | ||
| chrom = match_nochr_chrom[1] | ||
| pos = match_pos[1] | ||
| ref = match_ref[1] | ||
| alt = match_alt[1] | ||
| gene = match_gene_symbol[1] |
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Function intervar refactored with the following changes:
- Replace m.group(x) with m[x] for re.Match objects [×6] (
use-getitem-for-re-match-groups) - Replace manual loop counter with call to enumerate (
convert-to-enumerate) - Convert for loop into list comprehension (
list-comprehension) - Swap if/else branches (
swap-if-else-branches) - Remove unnecessary else after guard condition (
remove-unnecessary-else)
This removes the following comments ( why? ):
# print(obj)
| vv_url = md_utilities.get_vv_api_url() | ||
| if vv_url: | ||
| if vv_url := md_utilities.get_vv_api_url(): |
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Function check_vv_instance refactored with the following changes:
- Use named expression to simplify assignment and conditional (
use-named-expression)
| external_tools['ClinVar']['version'] = 'v{}'.format( | ||
| clinvar_version | ||
| ) | ||
| external_tools['ClinGenSpecificationRegistry']['version'] = 'v{}'.format( | ||
| clingen_version | ||
| ) | ||
| external_tools['OncoKBGenes']['version'] = 'v{}'.format( | ||
| oncokb_genes_version | ||
| ) | ||
| external_tools['ClinVar']['version'] = f'v{clinvar_version}' | ||
| external_tools['ClinGenSpecificationRegistry'][ | ||
| 'version' | ||
| ] = f'v{clingen_version}' | ||
| external_tools['OncoKBGenes']['version'] = f'v{oncokb_genes_version}' |
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Lines 190-198 refactored with the following changes:
- Replace call to format with f-string [×3] (
use-fstring-for-formatting)
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| match_obj = re.search(r'^(.+d[eu][lp])[ATCG]+$', variant) | ||
| if match_obj: | ||
| variant = match_obj.group(1) | ||
| else: | ||
| match_obj = re.search(r'^(.+del)[ATCG]+(ins[ACTG])$', variant) | ||
| if match_obj: | ||
| variant = match_obj.group(1) + match_obj.group(2) | ||
| if match_obj := re.search(r'^(.+d[eu][lp])[ATCG]+$', variant): | ||
| variant = match_obj[1] | ||
| elif match_obj := re.search(r'^(.+del)[ATCG]+(ins[ACTG])$', variant): | ||
| variant = match_obj[1] + match_obj[2] |
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Function clean_var_name refactored with the following changes:
- Use named expression to simplify assignment and conditional [×2] (
use-named-expression) - Replace m.group(x) with m[x] for re.Match objects [×3] (
use-getitem-for-re-match-groups) - Merge else clause's nested if statement into elif (
merge-else-if-into-elif)
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| match_object = re.search(r'^(\w{3})(\d+)(\w{3}|[X\*=])$', var) | ||
| if match_object: | ||
| if re.search('d[ue][pl]', match_object.group(3)): | ||
| return three2one[match_object.group(1).capitalize()] + \ | ||
| match_object.group(2) + \ | ||
| match_object.group(3) | ||
| if match_object := re.search(r'^(\w{3})(\d+)(\w{3}|[X\*=])$', var): | ||
| if re.search('d[ue][pl]', match_object[3]): | ||
| return ( | ||
| three2one[match_object[1].capitalize()] | ||
| + match_object[2] | ||
| + match_object[3] | ||
| ) | ||
| else: | ||
| return three2one[match_object.group(1).capitalize()] + \ | ||
| match_object.group(2) + \ | ||
| three2one[match_object.group(3).capitalize()] | ||
| match_object = re.search(r'^(\w{3})(\d+_)(\w{3})(\d+.+)$', var) | ||
| if match_object: | ||
| return three2one[match_object.group(1)].capitalize() + \ | ||
| match_object.group(2) + \ | ||
| three2one[match_object.group(3)].capitalize() + \ | ||
| match_object.group(4) | ||
| match_object = re.search(r'^(\w{3})(\d+)\w{3}fsTer\d+$', var) | ||
| if match_object: | ||
| return three2one[match_object.group(1)].capitalize() + \ | ||
| match_object.group(2) + \ | ||
| 'fs' | ||
| return ( | ||
| three2one[match_object[1].capitalize()] | ||
| + match_object[2] | ||
| + three2one[match_object[3].capitalize()] | ||
| ) | ||
| if match_object := re.search(r'^(\w{3})(\d+_)(\w{3})(\d+.+)$', var): | ||
| return ( | ||
| three2one[match_object[1]].capitalize() | ||
| + match_object[2] | ||
| + three2one[match_object[3]].capitalize() | ||
| + match_object[4] | ||
| ) | ||
| if match_object := re.search(r'^(\w{3})(\d+)\w{3}fsTer\d+$', var): | ||
| return three2one[match_object[1]].capitalize() + match_object[2] + 'fs' |
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Function three2one_fct refactored with the following changes:
- Use named expression to simplify assignment and conditional [×3] (
use-named-expression) - Replace m.group(x) with m[x] for re.Match objects [×13] (
use-getitem-for-re-match-groups)
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| match_object = re.search(r'^(\w{1})(\d+)([\w\*=]{1})$', var) | ||
| if match_object: | ||
| return one2three[match_object.group(1).capitalize()] + \ | ||
| match_object.group(2) + \ | ||
| one2three[match_object.group(3).capitalize()] | ||
| match_object = re.search(r'^(\w{1})(\d+)(d[ue][pl])$', var) | ||
| if match_object: | ||
| return one2three[match_object.group(1).capitalize()] + \ | ||
| match_object.group(2) + \ | ||
| match_object.group(3) | ||
| match_object = re.search(r'^(\w{1})(\d+_)(\w{1})(\d+.+)$', var) | ||
| if match_object: | ||
| return one2three[match_object.group(1).capitalize()] + \ | ||
| match_object.group(2) + \ | ||
| one2three[match_object.group(3).capitalize()] + \ | ||
| match_object.group(4) | ||
| if match_object := re.search(r'^(\w{1})(\d+)([\w\*=]{1})$', var): | ||
| return ( | ||
| one2three[match_object[1].capitalize()] | ||
| + match_object[2] | ||
| + one2three[match_object[3].capitalize()] | ||
| ) | ||
| if match_object := re.search(r'^(\w{1})(\d+)(d[ue][pl])$', var): | ||
| return ( | ||
| one2three[match_object[1].capitalize()] | ||
| + match_object[2] | ||
| + match_object[3] | ||
| ) | ||
| if match_object := re.search(r'^(\w{1})(\d+_)(\w{1})(\d+.+)$', var): | ||
| return ( | ||
| one2three[match_object[1].capitalize()] | ||
| + match_object[2] | ||
| + one2three[match_object[3].capitalize()] | ||
| + match_object[4] | ||
| ) |
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Function one2three_fct refactored with the following changes:
- Use named expression to simplify assignment and conditional [×3] (
use-named-expression) - Replace m.group(x) with m[x] for re.Match objects [×10] (
use-getitem-for-re-match-groups)
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| short_chr = get_short_chr_name(chr_name) | ||
| if short_chr: | ||
| if short_chr := get_short_chr_name(chr_name): |
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Function get_ncbi_chr_name refactored with the following changes:
- Use named expression to simplify assignment and conditional [×2] (
use-named-expression)
This removes the following comments ( why? ):
# print(ncbi_name)
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| res = curs.fetchone() | ||
| if res: | ||
| if res := curs.fetchone(): |
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Function get_common_chr_name refactored with the following changes:
- Use named expression to simplify assignment and conditional (
use-named-expression)
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| if re.search(rf'^[Cc][Hh][Rr]({nochr_captured_regexp})$', chr_name): | ||
| return True | ||
| return False | ||
| return bool(re.search(rf'^[Cc][Hh][Rr]({nochr_captured_regexp})$', chr_name)) |
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Function is_valid_full_chr refactored with the following changes:
- Lift code into else after jump in control flow (
reintroduce-else) - Replace if statement with if expression (
assign-if-exp) - Simplify boolean if expression (
boolean-if-exp-identity)
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| return match_obj.group(1) | ||
| return match_obj[1] |
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Function get_short_chr_name refactored with the following changes:
- Replace m.group(x) with m[x] for re.Match objects (
use-getitem-for-re-match-groups)
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| if re.search(rf'^({nochr_captured_regexp})$', chr_name): | ||
| return True | ||
| return False | ||
| return bool(re.search(rf'^({nochr_captured_regexp})$', chr_name)) |
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Function is_valid_chr refactored with the following changes:
- Lift code into else after jump in control flow (
reintroduce-else) - Replace if statement with if expression (
assign-if-exp) - Simplify boolean if expression (
boolean-if-exp-identity)
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| if re.search(r'^[Nn][Cc]_0000\d{2}\.\d{1,2}$', chr_name): | ||
| return True | ||
| return False | ||
| return bool(re.search(r'^[Nn][Cc]_0000\d{2}\.\d{1,2}$', chr_name)) |
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Function is_valid_ncbi_chr refactored with the following changes:
- Lift code into else after jump in control flow (
reintroduce-else) - Replace if statement with if expression (
assign-if-exp) - Simplify boolean if expression (
boolean-if-exp-identity)
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| return 'Match failed in {}'.format(text) | ||
| return f'Match failed in {text}' |
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Function get_value_from_tabix_file refactored with the following changes:
- Replace call to format with f-string [×2] (
use-fstring-for-formatting)
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| match_obj = re.search(r'^([A-Z][a-z]{2})(\d+)([A-Z][a-z]{2})$', p_name) | ||
| if match_obj: | ||
| return three2one[match_obj.group(1)], match_obj.group(2), three2one[match_obj.group(3)] | ||
| if match_obj := re.search( | ||
| r'^([A-Z][a-z]{2})(\d+)([A-Z][a-z]{2})$', p_name | ||
| ): | ||
| return three2one[match_obj[1]], match_obj[2], three2one[match_obj[3]] |
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Function decompose_missense refactored with the following changes:
- Use named expression to simplify assignment and conditional (
use-named-expression) - Replace m.group(x) with m[x] for re.Match objects [×3] (
use-getitem-for-re-match-groups)
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| score = re.split( | ||
| '{}'.format(sep), dbnsfp_record[score_index] | ||
| )[transcript_index] | ||
| score = re.split(f'{sep}', dbnsfp_record[score_index])[transcript_index] | ||
| if pred_index != score_index: | ||
| pred = predictors_translations[translation_mode][ | ||
| re.split( | ||
| '{}'.format(sep), | ||
| dbnsfp_record[pred_index] | ||
| )[transcript_index] | ||
| re.split(f'{sep}', dbnsfp_record[pred_index])[transcript_index] |
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Function getdbNSFP_results refactored with the following changes:
- Replace call to format with f-string [×2] (
use-fstring-for-formatting)
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| # returns most deleterious score of predictors | ||
| # when not found in desired transcript | ||
| j = 0 | ||
| k = 0 | ||
| best_score = threshold | ||
| for score in re.split(';', score): | ||
| for j, score in enumerate(re.split(';', score)): | ||
| if direction == 'lt': | ||
| if score != '.' and \ | ||
| float(score) < float(best_score): | ||
| best_score = score | ||
| k = j | ||
| else: | ||
| if score != '.' and \ | ||
| elif score != '.' and \ | ||
| float(score) > float(best_score): | ||
| best_score = score | ||
| k = j | ||
| j += 1 | ||
| best_score = score | ||
| k = j |
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Function get_most_other_deleterious_pred refactored with the following changes:
- Move assignment closer to its usage within a block (
move-assign-in-block) - Replace manual loop counter with call to enumerate (
convert-to-enumerate) - Merge else clause's nested if statement into elif (
merge-else-if-into-elif)
This removes the following comments ( why? ):
# when not found in desired transcript
# returns most deleterious score of predictors
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| value = float(val) | ||
| if predictor == 'sift': | ||
| value = 1-(float(val)) | ||
| value = 1-(float(val)) if predictor == 'sift' else float(val) |
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Function get_preditor_single_threshold_color refactored with the following changes:
- Move setting of default value for variable into
elsebranch (introduce-default-else) - Replace if statement with if expression (
assign-if-exp)
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| return match_object.group(1) | ||
| else: | ||
| match_object = re.search(r'_(\d+)[di]', g_name) | ||
| if match_object is not None: | ||
| return match_object.group(1) | ||
| else: | ||
| # case of single nt dels ins dup | ||
| match_object = re.search(r'^(\d+)[d]', g_name) | ||
| if match_object is not None: | ||
| return match_object.group(1) | ||
| return None | ||
| return match_object[1] | ||
| match_object = re.search(r'_(\d+)[di]', g_name) | ||
| if match_object is not None: | ||
| return match_object[1] | ||
| # case of single nt dels ins dup | ||
| match_object = re.search(r'^(\d+)[d]', g_name) | ||
| return match_object[1] if match_object is not None else None |
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Function compute_pos_end refactored with the following changes:
- Swap if/else branches [×4] (
swap-if-else-branches) - Remove unnecessary else after guard condition [×2] (
remove-unnecessary-else) - Replace m.group(x) with m[x] for re.Match objects [×3] (
use-getitem-for-re-match-groups) - Lift code into else after jump in control flow (
reintroduce-else) - Replace if statement with if expression (
assign-if-exp)
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| return match_object.group(1), match_object.group(2) | ||
| else: | ||
| match_object = re.search(r'^(\d+)[ATGC]>', name) | ||
| if match_object is not None: | ||
| return match_object.group(1), match_object.group(1) | ||
| else: | ||
| # single nt del or delins | ||
| match_object = re.search(r'^(\d+)[d]', name) | ||
| if match_object is not None: | ||
| return match_object.group(1), match_object.group(1) | ||
| else: | ||
| return match_object[1], match_object[2] | ||
| match_object = re.search(r'^(\d+)[ATGC]>', name) | ||
| if match_object is not None: | ||
| return match_object[1], match_object[1] | ||
| # single nt del or delins | ||
| match_object = re.search(r'^(\d+)[d]', name) | ||
| if match_object is not None: | ||
| return match_object[1], match_object[1] | ||
| # case where NM wt disagree with genomic wt | ||
| if re.search(r'^\d+=', name): | ||
| return '-1', '-1' | ||
| return None, None | ||
| return ('-1', '-1') if re.search(r'^\d+=', name) else (None, None) |
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Function compute_start_end_pos refactored with the following changes:
- Swap if/else branches [×6] (
swap-if-else-branches) - Remove unnecessary else after guard condition [×3] (
remove-unnecessary-else) - Replace m.group(x) with m[x] for re.Match objects [×6] (
use-getitem-for-re-match-groups) - Lift code into else after jump in control flow (
reintroduce-else) - Replace if statement with if expression (
assign-if-exp)
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| begin_txt = 'VariantValidator error: ' | ||
| if var == '': | ||
| begin_txt = '' | ||
| begin_txt = '' if var == '' else 'VariantValidator error: ' |
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Function danger_panel refactored with the following changes:
- Move setting of default value for variable into
elsebranch (introduce-default-else) - Replace if statement with if expression (
assign-if-exp)
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| # to print general info do not send var neither id_var | ||
| # Newly created variant: | ||
| c = 'c.' | ||
| if re.search(r'N[MR]_', var): | ||
| c = '' | ||
| c = '' if re.search(r'N[MR]_', var) else 'c.' |
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Function info_panel refactored with the following changes:
- Move setting of default value for variable into
elsebranch (introduce-default-else) - Replace if statement with if expression (
assign-if-exp)
This removes the following comments ( why? ):
# Newly created variant:
# to print general info do not send var neither id_var
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| if checked_url: | ||
| return checked_url | ||
| else: | ||
| if not checked_url: | ||
| checked_url = test_vv_api_url( | ||
| urls['variant_validator_api_hello'], | ||
| urls['variant_validator_api'] | ||
| ) | ||
| return checked_url | ||
| return checked_url | ||
| else: | ||
| # the other way around | ||
| checked_url = test_vv_api_url( | ||
| urls['variant_validator_api_hello'], | ||
| urls['variant_validator_api'] | ||
| ) | ||
| if checked_url: | ||
| if checked_url := test_vv_api_url( | ||
| urls['variant_validator_api_hello'], urls['variant_validator_api'] | ||
| ): | ||
| return checked_url | ||
| if checked_url := test_vv_api_url( | ||
| urls['variant_validator_api_hello_backup'], | ||
| urls['variant_validator_api_backup'], | ||
| ): | ||
| return checked_url | ||
| else: | ||
| checked_url = test_vv_api_url( | ||
| urls['variant_validator_api_hello_backup'], | ||
| urls['variant_validator_api_backup'] | ||
| ) | ||
| if checked_url: | ||
| return checked_url | ||
| else: |
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Function get_vv_api_url refactored with the following changes:
- Swap if/else to remove empty if body (
remove-pass-body) - Hoist repeated code outside conditional statement (
hoist-statement-from-if) - Use named expression to simplify assignment and conditional [×2] (
use-named-expression) - Remove unnecessary else after guard condition (
remove-unnecessary-else)
This removes the following comments ( why? ):
# the other way around
| assert client.get( | ||
| '/auth/variant_list/{}'.format( | ||
| list_name, | ||
| ) | ||
| ).status_code == http_code | ||
| assert client.get(f'/auth/variant_list/{list_name}').status_code == http_code |
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Function test_variant_list refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
| assert client.get('/gene/{}'.format(name[0])).status_code == 200 | ||
| assert client.get(f'/gene/{name[0]}').status_code == 200 |
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Function test_gene_page refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
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| print(response.headers['Location'] + 'http://localhost/{}'.format(url)) | ||
| assert 'http://localhost/{}'.format(url) == response.headers['Location'] | ||
| print(response.headers['Location'] + f'http://localhost/{url}') | ||
| assert f'http://localhost/{url}' == response.headers['Location'] |
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Function test_search_engine refactored with the following changes:
- Replace call to format with f-string [×2] (
use-fstring-for-formatting)
| assert client.get('/api/variant/{}/browser/'.format(variant_id[0])).status_code == 200 | ||
| assert client.get(f'/api/variant/{variant_id[0]}/browser/').status_code == 200 |
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Function test_variant_page refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
| print('-{}'.format(totest)) | ||
| print(f'-{totest}') |
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Function test_format_mirs refactored with the following changes:
- Replace call to format with f-string (
use-fstring-for-formatting)
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
| if match_obj: | ||
| password = match_obj.group(1) | ||
| if match_obj := re.search( | ||
| r'(?!^[0-9]*$)(?!^[a-z]*$)(?!^[A-Z]*$)(?!^[a-zA-Z]*$)(?!^[a-z0-9]*$)(?!^[A-Z0-9]*$)^(.{8,})$', |
Check failure
Code scanning / CodeQL
Unmatchable dollar in regular expression Error
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