From edcf0fffee264fed5c9affd6ca93c2516d3ecaa4 Mon Sep 17 00:00:00 2001 From: Char-Al Date: Wed, 21 Feb 2024 15:50:25 +0100 Subject: [PATCH 1/3] Fix Typo --- seal/templates/analysis/sample.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/seal/templates/analysis/sample.html b/seal/templates/analysis/sample.html index 9074feb..c2e6dee 100644 --- a/seal/templates/analysis/sample.html +++ b/seal/templates/analysis/sample.html @@ -1225,7 +1225,7 @@

Comments ()

if(data["INTRON"] == null) { return "NA"; } - return "Inton " + data["INTRON"].split("/")[0]; + return "Intron " + data["INTRON"].split("/")[0]; } return "Exon " + data["EXON"].split("/")[0]; }, From ca2ef76995d1ba13b7aeac9c1466cf1465277d1a Mon Sep 17 00:00:00 2001 From: Char-Al Date: Wed, 21 Feb 2024 16:40:51 +0100 Subject: [PATCH 2/3] Fix: unlink locker when ftp not reached --- seal/schedulers.py | 78 ++++++++++++++++++++++++---------------------- 1 file changed, 41 insertions(+), 37 deletions(-) diff --git a/seal/schedulers.py b/seal/schedulers.py index f7f5a07..a9a7ae9 100644 --- a/seal/schedulers.py +++ b/seal/schedulers.py @@ -681,40 +681,44 @@ def check_clinvar(genome="GRCh37"): lockFile = open(path_locker, 'x') lockFile.close() - ftp=FTP('ftp.ncbi.nlm.nih.gov') - ftp.login() - ftp.cwd(f'pub/clinvar/vcf_{genome}') - - ls = ftp.nlst() - for i in ls: - r = re.compile("clinvar_([0-9]+).vcf.gz$") - match = r.search(i) - app.logger.info(f" - file : {i}") - if match: - app.logger.info(f" - match : {match.group(1)}") - version = match.group(1) - file = match.group(0) - - if not Clinvar.query.filter_by(version=version, genome=genome.lower()).one_or_none(): - app.logger.info(f" - new clinvar") - vcf_path = Path(app.root_path).joinpath(f'static/temp/clinvar/{genome}') - vcf_path = vcf_path.joinpath(file) - t = 0 - while t < 10: - try: - app.logger.info(f" - download attempt : {t}") - with open(f'{vcf_path}', 'wb') as fp: - ftp.retrbinary(f'RETR {file}', fp.write) - Thread(target=update_clinvar_thread, args=(vcf_path, int(version), genome.lower(), )).start() - app.logger.info(f" - thread launched") - t=10 - except Exception as e: - app.logger.info(f" - download filed retry") - app.logger.error(e) - ftp.close() - ftp=FTP('ftp.ncbi.nlm.nih.gov') - ftp.login() - ftp.cwd(f'pub/clinvar/vcf_{genome}') - t+=1 - app.logger.info("END CLINVAR UPDATE") - path_locker.unlink() \ No newline at end of file + try: + ftp=FTP('ftp.ncbi.nlm.nih.gov') + ftp.login() + ftp.cwd(f'pub/clinvar/vcf_{genome}') + except Exception as e: + app.logger.error(e) + else: + ls = ftp.nlst() + for i in ls: + r = re.compile("clinvar_([0-9]+).vcf.gz$") + match = r.search(i) + app.logger.info(f" - file : {i}") + if match: + app.logger.info(f" - match : {match.group(1)}") + version = match.group(1) + file = match.group(0) + + if not Clinvar.query.filter_by(version=version, genome=genome.lower()).one_or_none(): + app.logger.info(f" - new clinvar") + vcf_path = Path(app.root_path).joinpath(f'static/temp/clinvar/{genome}') + vcf_path = vcf_path.joinpath(file) + t = 0 + while t < 10: + try: + app.logger.info(f" - download attempt : {t}") + with open(f'{vcf_path}', 'wb') as fp: + ftp.retrbinary(f'RETR {file}', fp.write) + Thread(target=update_clinvar_thread, args=(vcf_path, int(version), genome.lower(), )).start() + app.logger.info(f" - thread launched") + t=10 + except Exception as e: + app.logger.info(f" - download filed retry") + app.logger.error(e) + ftp.close() + ftp=FTP('ftp.ncbi.nlm.nih.gov') + ftp.login() + ftp.cwd(f'pub/clinvar/vcf_{genome}') + t+=1 + finally: + app.logger.info("END CLINVAR UPDATE") + path_locker.unlink() \ No newline at end of file From 48958fa783553b33ed07feb6bf23217710a77f6b Mon Sep 17 00:00:00 2001 From: Char-Al Date: Wed, 21 Feb 2024 16:45:41 +0100 Subject: [PATCH 3/3] Update About --- seal/templates/essentials/about.html | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/seal/templates/essentials/about.html b/seal/templates/essentials/about.html index 6806af7..c2bd4d9 100644 --- a/seal/templates/essentials/about.html +++ b/seal/templates/essentials/about.html @@ -84,6 +84,24 @@

License

Releases

+

v1.1.9 [February 21, 2024]

+ +

This minor version mainly enhances fix some bugs.

+

Fixes

+
    +
  • Fix some typo
    • +
  • Fix locker when ftp of ncbi not reached
    • +
  • Update Links for GnomAD
    • +
+ +

Known Issues

+
    +
  • Initialisation of database
    • +
+ +
+ +

v1.1.8 [November 08, 2023]

This minor version mainly enhances fix some bugs.