From 34055a1d6978228f089858ddbeba97dc88019c58 Mon Sep 17 00:00:00 2001 From: MarvinDo Date: Tue, 16 Jan 2024 15:10:16 +0100 Subject: [PATCH] changelog update --- .../.nfs000001309139a197000007f1 | 69 ------------------- .../webapp/templates/doc/changelog.html | 5 -- .../webapp/templates/index.html | 49 +------------ 3 files changed, 2 insertions(+), 121 deletions(-) delete mode 100755 src/frontend_celery/.nfs000001309139a197000007f1 diff --git a/src/frontend_celery/.nfs000001309139a197000007f1 b/src/frontend_celery/.nfs000001309139a197000007f1 deleted file mode 100755 index 5e8b56a3..00000000 --- a/src/frontend_celery/.nfs000001309139a197000007f1 +++ /dev/null @@ -1,69 +0,0 @@ -#!/bin/bash -set -e -set -o pipefail - - -helpFunction() -{ - echo "" - echo "Usage: $0 -w env" - echo "This script starts the heredivar frontend gunicorn or development server" - echo -e "\t-w Provide 'dev' for development server and 'prod' for production gunicorn server." - exit 1 # Exit script after printing help -} - -while getopts "w:" opt -do - case "$opt" in - w ) we="$OPTARG" ;; - ? ) helpFunction ;; # Print helpFunction in case parameter is non-existent - esac -done - -# Print helpFunction in case parameters are empty -if [ -z "$we" ] -then - echo "Some or all of the parameters are empty"; - helpFunction -fi - - -# set paths -SCRIPT=$(readlink -f "$0") -ROOT=$(dirname $(dirname $(dirname "$SCRIPT"))) -cd $ROOT -pwd - - -export WEBAPP_ENV=$we -if [ -z "${WEBAPP_ENV}" ] -then - echo Environment variable WEBAPP_ENV not set. - exit 1 -fi - -echo starting Heredivar in "${WEBAPP_ENV}" mode - - -source .venv/bin/activate - -if [ "${WEBAPP_ENV}" == "dev" ] -then - cd src/frontend_celery - python3 main.py -fi - -if [ "${WEBAPP_ENV}" == "prod" ] -then - #export CURL_CA_BUNDLE="" - set -o allexport - extension=env_ - source $ROOT/.$extension$WEBAPP_ENV - set +o allexport - - logsdir=$ROOT/logs - mkdir -p $logsdir/gunicorn-access-logs - mkdir -p $logsdir/gunicorn-error-logs - gunicorn -b $HOST:$PORT -w 4 'webapp:create_app()' --access-logfile $logsdir/gunicorn-access-logs/access.log --error-logfile $logsdir/gunicorn-error-logs/error.log # heredivar.uni-koeln.de:8000 - #gunicorn -b SRV018.img.med.uni-tuebingen.de:8001 -w 1 'webapp:create_app()' -fi \ No newline at end of file diff --git a/src/frontend_celery/webapp/templates/doc/changelog.html b/src/frontend_celery/webapp/templates/doc/changelog.html index eceb1eed..30c87b59 100644 --- a/src/frontend_celery/webapp/templates/doc/changelog.html +++ b/src/frontend_celery/webapp/templates/doc/changelog.html @@ -62,11 +62,6 @@

Changelog

  • In BRCA2 v1.0.0 criteria supporting strength was not selectable
  • Sometimes, the classification scheme was not changeable in consensus classifications
    • - Known issues: -
    v 1.5 (17.11.2023)
    diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html index c66ab41e..bcbf2d0a 100644 --- a/src/frontend_celery/webapp/templates/index.html +++ b/src/frontend_celery/webapp/templates/index.html @@ -92,7 +92,8 @@

    Overview

    Changelog

    -
    v 1.7 ()
    +
    v 1.7 (16.01.2024)
    +
    !! The automatic classification algorithm is currently under construction. HerediVar is already prepared for it. Thus, you might encounter disabled buttons or dummy data. It will be enabled in a future update
    General changes:
      @@ -123,52 +124,6 @@

      Changelog

    • HerediCare priors, log likelihood, segregation & cooccurance are not available
    - -
    v 1.6.1 (11.01.2024)
    -
    - Bugfixes: -
      -
    • Searching for 4M criterium with include_heredicare option would result in an error
      • -
    • Searching for class 4 consensus classification with include_heredicare option previously resulted in consensus class 4 and heredicare class 3+
      • -
    -
    -
    v 1.6 (10.01.2024)
    -
    !! The automatic classification algorithm is currently under construction. HerediVar is already prepared for it. Thus, you might encounter disabled buttons or dummy data. It will be enabled in a future update
    -
    - General changes: -
      -
    • Added form to create structural variants: DEL, DUP, INV
      • -
    • Added structural variants to browse variants table
      • -
    • Added START, END, SVTYPE, IMPRECISE info columns to vcf with structural variants
      • -
    • Added the general comment to the classified variants download
      • -
    • Added a separate download link for all classified structural variants
      • -
    • Added structural variants track to IGV
      • -
    • Added the coldspot annotation
      • -
    • Added variant search which allows the user to search directly for a specific variant using this format: chrom-pos-ref-alt OR chrom-start-end-sv_type in case of structural variants
      • -
    • Changed External ID search to overall ID search. It now also allows to search for heredivar variant ids.
      • -
    • Update search help
      • -
    • Added variant type search option
      • -
    • Updated ClinVar to v. 20240207
      • -
    - Bugfixes: -
      -
    • Fixed a bug where the criterium strength addition to the label would reset when the default strength was not its original strength.
      • -
    • Fixed the order of selectable criteria strengths on the classify variants page
      • -
    • Fixed a bug when submitting 4M classifications
      • -
    • Previously, updates to ClinVar submissions were not working & removed the 'customAssertionScore' from ClinVar submissions
      • -
    • Fixed a bug when trying to add all variants from a search to a list
      • -
    • In BRCA2 v1.0.0 criteria supporting strength was not selectable
      • -
    • Sometimes, the classification scheme was not changeable in consensus classifications
      • -
    • BRCA1 v1.0.0 PP1 criterium was missing strength selection and PP4 criterium was missing very strong strength
      • -
    • BRCA2 v1.0.0 PP1 and PP4 criteria were missing very strong strength
      • -
    • Fixed a bug when a standard or read only user was accessing the variant details page when a ClinVar submission was unfinished
      • -
    - Known issues: -
      -
    • HerediCare Center specific classifications are not available
      • -
    • HerediCare priors, log likelihood, segregation & cooccurance are not available
      • -
    -
    previous changelog