update base image to fix vulnerabilities

Dockerfile

@@ -1,4 +1,4 @@
-FROM continuumio/miniconda3:4.10.3
+FROM continuumio/miniconda3
 
 WORKDIR /usr/src/caddie/
 
@@ -7,49 +7,21 @@ ENV PYTHONUNBUFFERED 1
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
 
-# install gcc
 RUN apt-get update
 RUN apt-get -y install build-essential
-RUN apt-get -y install python-dev python3-dev
 RUN apt-get -y install gcc
 
-# RUN apt-get update
-# RUN apt-get install -y supervisor nginx
-# RUN apt-get install -y libgtk-3-dev
-# RUN apt-get install -y wget
-
-
-RUN conda install -y conda=4.10.3
 RUN conda install -c conda-forge -y graph-tool
 
-# setuptools 58 does not support use_2to3
-# RUN pip install setuptools==57.5.0
-# RUN pip install -r /usr/src/caddie/requirements.txt
-# RUN pip install gunicorn
-
-
-
-
-# OLD
 RUN apt-get update
 RUN apt-get install -y supervisor nginx
-RUN apt-get install -y libgtk-3-dev
 RUN apt-get install wget
 
 COPY ./requirements.txt /usr/src/caddie/requirements.txt
 
-# RUN conda install -y conda=4.3.16
-# RUN conda install -c conda-forge -y graph-tool=2.32
-
-RUN pip install -r /usr/src/caddie/requirements.txt
-RUN pip install gunicorn
-
-
-
-
-
-
-# RUN pyensembl install --release 106 --species human
+# RUN pip3 install setuptools==57
+RUN pip3 install -r /usr/src/caddie/requirements.txt
+RUN pip3 install gunicorn
 
 COPY ./supervisord.conf /etc/supervisor/conf.d/supervisord.conf
 COPY ./docker-entrypoint.sh /entrypoint.sh

caddie/utils/vcfUtils.py

@@ -1,6 +1,6 @@
-import vcf   # VCF 4.1, 4-2
+# import vcf   # VCF 4.1, 4-2
 # import vcfpy  # VCF 4.3
-import vap
+# import vap
 from sqlalchemy import create_engine
 
 
@@ -12,7 +12,7 @@ def __read_pyvcf(file):
         :param file:
         :return: vcf reader object
         """
-        return vcf.Reader(fsock=file)
+        # return vcf.Reader(fsock=file)
 
     @staticmethod
     def __annotate(vcf_reader):
@@ -32,7 +32,8 @@ def __annotate(vcf_reader):
         annotations = []
         for record in vcf_reader:
             for alt in record.ALT:
-                annotation = vap.annotate_variant(conn, f'chr{record.CHROM}', record.POS, record.REF, alt)
+                # annotation = vap.annotate_variant(conn, f'chr{record.CHROM}', record.POS, record.REF, alt)
+                annotation = None
                 if annotation is not None:
                     annotations.append((record, annotation))
         return annotations

docker-compose.yml

@@ -18,7 +18,7 @@ services:
       - db
       - redis
   db:
-    image: postgres
+    image: postgres:15
     restart: always
     hostname: db
     networks:

requirements.txt

@@ -19,69 +19,30 @@ flake8-quotes==3.0.0
 gunicorn==20.1.0
 mccabe==0.6.1
 networkx==2.5
-pandas==1.1.5
-psycopg2-binary==2.9.6
+numpy==1.26.4
+pandas==1.3.5
+psycopg2-binary
 # pycairo==1.20.1
 pycodestyle==2.5.0
 # pycosat==0.6.3
 pyflakes==2.1.1
 # PyGObject==3.40.1
 # pyparsing==2.4.7
-pysam==0.21.0
+pysam
 python-dateutil==2.8.1
 pytz==2019.3
-PyVCF==0.6.8
+# PyVCF==0.6.8
 redis==3.4.1
 rq==1.3.0
 six==1.15.0
 SQLAlchemy==1.3.23
 sqlparse==0.3.1
 urllib3==1.25.10
-vcf-annotate-polyphen==0.1.2
-vcfpy==0.13.3
-
+# vcf-annotate-polyphen
+# vcfpy
 # pysam==0.21.0
 deepmerge==0.3.0
 # pyensembl==2.0.0
 #domino-python==0.1.1
 
 
-
-# asgiref==3.2.7
-# certifi==2020.6.20
-# chardet==3.0.4
-# click==7.1.2
-# decorator==4.4.2
-# Django==3.0.5
-# django-cors-headers==3.4.0
-# django-redis==4.11.0
-# django-rq-dashboard==0.3.3 
-# djangorestframework==3.11.0
-# djangorestframework-camel-case==1.1.2
-# entrypoints==0.3
-# flake8==3.7.9
-# flake8-quotes==3.0.0
-# idna==2.10
-# mccabe==0.6.1
-# networkx==2.4
-# numpy==1.19.5
-# pandas==1.1.5
-# psycopg2-binary==2.9.6
-# pycodestyle==2.5.0
-# pyflakes==2.1.1
-# python-dateutil==2.8.2
-# pytz==2020.1
-# redis==3.4.1
-# requests
-# rq==1.3.0
-# six==1.15.0
-# sqlparse==0.3.1
-# urllib3==1.25.10
-# pyvcf==0.6.8
-# sqlalchemy==1.3.23
-# vcf-annotate-polyphen==0.1.2
-# vcfpy==0.13.3
-# pysam==0.21.0
-# deepmerge==0.3.0
-# # pyensembl==2.0.0
-# #domino-python==0.1.1