Sourcery refactored master branch #39
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -91,16 +91,16 @@ def litvar(): | |
| # print(article) | ||
| if article['authors'][0]: | ||
| pmid = int(article['pmid']) | ||
| 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] = {'title': ''} | ||
| return render_template( | ||
| 'ajax/litvar.html', | ||
| urls=md_utilities.urls, | ||
|
|
@@ -118,9 +118,8 @@ def litvar(): | |
|
|
||
| @bp.route('/litvar2', methods=['POST']) | ||
| def litvar2(): | ||
| if match_rsid := re.search(r'^(rs\d+)$', request.form['rsid']): | ||
| rsid = match_rsid[1] | ||
|
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| # if re.search(r'^rs\d+$', request.form['rsid']): | ||
| header = md_utilities.api_agent | ||
| # rsid = request.form['rsid'] | ||
|
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@@ -186,21 +185,20 @@ def litvar2(): | |
| if 'authors' in article and \ | ||
| len(article['authors']) > 0: | ||
| pmid = int(article['pmid']) | ||
| pubmed_info[pmid] = { | ||
| 'title': article['title'], | ||
| 'journal': article['journal'], | ||
| 'year': article['year'], | ||
| 'author': article['authors'][0], | ||
| } | ||
| except Exception: | ||
| for pubmed_id in litvar_data['pmids']: | ||
| pmid = int(pubmed_id) | ||
| pubmed_info[pmid] = {'title': ''} | ||
| if not pubmed_info: | ||
| for pubmed_id in litvar_data['pmids']: | ||
| pmid = int(pubmed_id) | ||
| pubmed_info[pmid] = {'title': ''} | ||
| # get litvar direct link of rsid | ||
| litvar_sensor_url = "{0}{1}".format( | ||
| md_utilities.urls['ncbi_litvar_apiv2_sensor'], rsid | ||
|
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@@ -256,9 +254,9 @@ def defgen(): | |
| match_varid = re.search(r'^(\d+)$', request.form['vfid']) | ||
| if match_varid and \ | ||
| match_genome: | ||
| variant_id = match_varid[1] | ||
| # genome = request.form['genome'] | ||
| genome = match_genome[1] | ||
|
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|
||
| db = get_db() | ||
| curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor) | ||
| # get all variant_features and gene info | ||
|
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@@ -274,19 +272,28 @@ def defgen(): | |
| (variant_id, genome) | ||
| ) | ||
| vf = curs.fetchone() | ||
| rsid = 'rs{0}'.format(vf['dbsnp_id']) if vf['dbsnp_id'] else '' | ||
| file_content = ( | ||
| "GENE;VARIANT;A_ENREGISTRER;ETAT;RESULTAT;VARIANT_P;\ | ||
| VARIANT_C;ENST;NM;POSITION_GENOMIQUE;CLASSESUR5;CLASSESUR3;COSMIC;RS;\ | ||
| REFERENCES;CONSEQUENCES;COMMENTAIRE;CHROMOSOME;GENOME_REFERENCE;\ | ||
| NOMENCLATURE_HGVS;LOCALISATION;SEQUENCE_REF;LOCUS;ALLELE1;ALLELE2\r\n" | ||
| + "{0};{1}:c.{2};;;;p.{3};c.{2};{4};{1};{5};\ | ||
| ;;;{6};;{7};;chr{8};{9};chr{8}:g.{10};{11} {12};;;;\r\n".format( | ||
| vf['gene_symbol'], | ||
| vf['refseq'], | ||
| vf['c_name'], | ||
| vf['p_name'], | ||
| vf['enst'], | ||
| vf['pos'], | ||
| rsid, | ||
| vf['prot_type'], | ||
| vf['chr'], | ||
| genome, | ||
| vf['g_name'], | ||
| vf['start_segment_type'], | ||
| vf['start_segment_number'], | ||
| ) | ||
| ) | ||
| # print(file_content) | ||
| app_path = os.path.dirname(os.path.realpath(__file__)) | ||
|
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@@ -309,12 +316,9 @@ def defgen(): | |
| md_utilities.send_error_email( | ||
| md_utilities.prepare_email_html( | ||
| 'MobiDetails Ajax error', | ||
| f'<p>DefGen file generation failed in {os.path.basename(__file__)} (no variant_id)</p>', | ||
| ), | ||
| '[MobiDetails - Ajax Error]', | ||
| ) | ||
| return """ | ||
| <div class="w3-blue w3-ripple w3-padding-16 w3-large w3-center" style="width:100%"> | ||
|
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@@ -343,12 +347,12 @@ def intervar(): | |
| match_ref and \ | ||
| match_alt and \ | ||
| match_gene_symbol: | ||
| 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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||
| header = md_utilities.api_agent | ||
| if len(ref) > 1 or len(alt) > 1: | ||
| return 'No wintervar for indels' | ||
|
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@@ -396,17 +400,12 @@ def intervar(): | |
| headers=header | ||
| ).data.decode('utf-8') | ||
| ) | ||
| for i, obj in enumerate(intervar_list): | ||
| # some housekeeping to get proper strings | ||
| obj = obj.replace('{', '').replace('}', '') | ||
| obj = '{{{}}}'.format(obj) | ||
| intervar_list[i] = obj | ||
| intervar_data = [json.loads(obj) for obj in intervar_list] | ||
| except Exception as e: | ||
| md_utilities.send_error_email( | ||
| md_utilities.prepare_email_html( | ||
|
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@@ -465,31 +464,30 @@ def intervar(): | |
| key, | ||
| md_utilities.acmg_criteria[key] | ||
| ) | ||
| if intervar_acmg is None: | ||
| return "<span>No wintervar class</span>" | ||
| db = get_db() | ||
| curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor) | ||
| curs.execute( | ||
| """ | ||
| SELECT html_code | ||
| FROM valid_class | ||
| WHERE acmg_translation = %s | ||
| """, | ||
| (intervar_acmg.lower(),) | ||
| ) | ||
| res = curs.fetchone() | ||
| close_db() | ||
| return """ | ||
| <span style='color:{0};'>{1}</span> | ||
| <span> with the following criteria:</span><br /><br /> | ||
| <div class='w3-row-padding w3-center'>{2}</div><br /> | ||
| <div id='acmg_info'></div> | ||
| """.format( | ||
| res['html_code'], | ||
| intervar_acmg, | ||
| intervar_criteria | ||
| ) | ||
| else: | ||
| md_utilities.send_error_email( | ||
| md_utilities.prepare_email_html( | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -48,8 +48,7 @@ def check_api_key(api_key=None): | |
|
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| @bp.route('/api/service/vv_instance', methods=['GET']) | ||
| def check_vv_instance(): | ||
| if vv_url := md_utilities.get_vv_api_url(): | ||
|
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|
||
| if vv_url == md_utilities.urls['variant_validator_api']: | ||
| return jsonify( | ||
| variant_validator_instance='Running genuine VV server', | ||
|
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@@ -76,47 +75,57 @@ def api_variant_exists(variant_ghgvs=None): | |
| return jsonify(mobidetails_error='No variant submitted') | ||
| variant_regexp = md_utilities.regexp['variant'] | ||
| chrom_regexp = md_utilities.regexp['ncbi_chrom'] | ||
| if not ( | ||
| match_variant_ghgvs := re.search( | ||
| rf'^({chrom_regexp}):g\.({variant_regexp})$', | ||
| urllib.parse.unquote(variant_ghgvs), | ||
| ) | ||
| ): | ||
| return jsonify(mobidetails_error='Malformed query, please check your input') | ||
| db = get_db() | ||
| chrom, genome_version = md_utilities.get_common_chr_name( | ||
| db, match_variant_ghgvs[1] | ||
| ) | ||
| if chrom and \ | ||
| genome_version: | ||
| pattern = match_variant_ghgvs[2] | ||
| curs = db.cursor(cursor_factory=psycopg2.extras.DictCursor) | ||
| curs.execute( | ||
| """ | ||
| SELECT feature_id | ||
| FROM variant | ||
| WHERE chr = %s | ||
| AND g_name = %s | ||
| AND genome_version = %s | ||
| """, | ||
| (chrom, pattern, genome_version) | ||
| ) | ||
| res = curs.fetchone() | ||
| if res is not None: | ||
| close_db() | ||
| return jsonify( | ||
| mobidetails_id=res['feature_id'], | ||
| url='{0}{1}'.format( | ||
| request.host_url[:-1], | ||
| url_for( | ||
| 'api.variant', | ||
| variant_id=res['feature_id'], | ||
| caller='browser' | ||
| ) | ||
| ) | ||
| ) | ||
| else: | ||
| close_db() | ||
| checked_var_ghgvs = '{0}:g.{1}'.format( | ||
| match_variant_ghgvs[1], match_variant_ghgvs[2] | ||
| ) | ||
| return jsonify( | ||
| mobidetails_warning=f'The variant {checked_var_ghgvs} does not exist yet in MD' | ||
| ) | ||
| else: | ||
| return jsonify( | ||
| mobidetails_error=f'The chromosome {match_variant_ghgvs[1]} does not exist in MD' | ||
| ) | ||
|
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This removes the following comments ( why? ): |
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| # ------------------------------------------------------------------- | ||
| # api - variant | ||
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Function
litvarrefactored with the following changes:merge-dict-assign)