Merge pull request #120 from EGA-archive/upgrade

Forcing the merge, not waiting for the tests to complete.

deploy/bootstrap/requirements.txt

@@ -2,6 +2,6 @@ bcrypt==3.1.7
 cffi==1.13.2
 docopt==0.6.2
 pycparser==2.19
-PyYAML==5.3
+PyYAML==5.4
 ruamel.yaml==0.16.6
 six==1.14.0

docs/requirements.txt

@@ -7,13 +7,13 @@ commonmark==0.9.1
 docutils==0.16
 idna==2.8
 imagesize==1.2.0
-Jinja2==2.10.3
+Jinja2==2.11.3
 MarkupSafe==1.1.1
 packaging==20.0
-Pygments==2.5.2
+Pygments==2.7.4
 pyparsing==2.4.6
 pytz==2019.3
-PyYAML==5.3
+PyYAML==5.4
 recommonmark==0.6.0
 requests==2.22.0
 six==1.14.0

ingestion/Dockerfile

@@ -1,7 +1,7 @@
 ##########################
 ## Build env, it works with debian buster 3.8
 ##########################
-FROM python:slim as BUILD
+FROM python:3.9-slim as BUILD
 
 ENV DEBIAN_FRONTEND noninteractive
 
@@ -23,7 +23,7 @@ RUN pip install /root/LocalEGA
 ##########################
 ## Final image
 ##########################
-FROM python:slim
+FROM python:3.9-slim
 
 LABEL maintainer "EGA System Developers"
 LABEL org.label-schema.schema-version="1.0"
@@ -36,7 +36,7 @@ RUN apt-get update && \
 		libpq5 \
 	&& rm -rf /var/lib/apt/lists/*
 
-COPY --from=BUILD usr/local/lib/python3.8/ usr/local/lib/python3.8/
+COPY --from=BUILD usr/local/lib/python3.9/ usr/local/lib/python3.9/
 COPY --from=BUILD /usr/local/bin/ega-* /usr/local/bin/
 
 ARG LEGA_UID=1000

ingestion/requirements.txt

@@ -1,21 +1,37 @@
 AMQPStorm==2.7.2
 bcrypt==3.1.7
-botocore==1.14.7
 boto3==1.11.7
+botocore==1.14.7
 certifi==2020.4.5.1
 cffi==1.14.0
 chardet==3.0.4
-crypt4gh==1.3
-cryptography==2.9.2
+crypt4gh==1.5
+cryptography==3.2
 docopt==0.6.2
+#docutils==0.15.2
 idna==2.9
+jmespath==0.10.0
 pamqp==2.3.0
 psycopg2-binary==2.8.5
 pycparser==2.20
 PyNaCl==1.3.0
-PyYAML==5.3.1
+python-dateutil==2.8.1
+PyYAML==5.4
 requests==2.23.0
 s3transfer==0.3.1
 six==1.14.0
 urllib3==1.25.9
-crypt4gh==1.3
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