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feat(openchallenges): add Mariadb Connection and Load the EDAM Concepts #2680

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feat(openchallenges): add Mariadb Connection and Load the EDAM Concepts #2680

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11a8e80
add mariadb connection
mdsage1 May 14, 2024
31a4bef
add the dataframe input
mdsage1 May 15, 2024
74e2450
Load the data to the table
mdsage1 May 15, 2024
33cc7de
add mariadb required library
mdsage1 May 17, 2024
26211c2
update to pip command
mdsage1 May 17, 2024
0a6bb0b
update project.json
mdsage1 May 17, 2024
8c652f1
add mariadb packaging
mdsage1 May 17, 2024
9bcd9e9
remove binaries
mdsage1 May 17, 2024
a384fcc
add pip command to prepare
mdsage1 May 17, 2024
9e779fa
update prepare format
mdsage1 May 17, 2024
69c5f9f
make prepare command plural
mdsage1 May 17, 2024
cb453b1
add install of maria db connector
mdsage1 May 17, 2024
631f3d2
update mariadb prep commands
mdsage1 May 17, 2024
77c7693
update env prep
mdsage1 May 17, 2024
3b5f6a8
change config for mariaDB
mdsage1 May 17, 2024
7842cd6
revert env prep
mdsage1 May 17, 2024
a65676f
fix command so its plural
mdsage1 May 17, 2024
ce17395
add commands to prepare-python
mdsage1 May 20, 2024
5f0332e
remove brackets
mdsage1 May 20, 2024
0da3bbd
change pip wheel command
mdsage1 May 20, 2024
3268c14
remove install for test
mdsage1 May 20, 2024
552cf2d
Merge branch 'Sage-Bionetworks:main' into load_to_mariadb
mdsage1 Jun 21, 2024
e8391fa
update docker image system dependencies
mdsage1 Jun 21, 2024
50cfa9c
remove trailing white spaces
mdsage1 Jun 21, 2024
970048f
remove trailing whitespace
mdsage1 Jun 21, 2024
c626cac
Merge branch 'Sage-Bionetworks:main' into load_to_mariadb
mdsage1 Aug 1, 2024
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7 changes: 5 additions & 2 deletions apps/openchallenges/edam-etl/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,12 @@ RUN groupadd --gid "$USER_GID" "$USERNAME" \
&& apt-get update -qq -y && export DEBIAN_FRONTEND=noninteractive \
&& apt-get install --no-install-recommends -qq -y \
gosu \
libmariadb-dev \
gcc \
&& apt-get -y autoclean \
&& apt-get -y autoremove \
&& rm -rf /var/lib/apt/lists/*
&& rm -rf /var/lib/apt/lists/*


WORKDIR ${APP_DIR}
COPY src src/
Expand All @@ -24,7 +27,7 @@ COPY pyproject.toml poetry.lock ./
# See /workspaces/sage-monorepo/tools/devcontainers/sage/.devcontainer/Dockerfile
RUN pip install --no-cache-dir poetry==1.6.1 \
&& poetry config --local virtualenvs.create false \
&& poetry install --with prod --no-root --no-interaction --no-ansi \
&& poetry install --no-root --no-interaction --no-ansi \
&& pip cache purge

WORKDIR /
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