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Merge pull request #25 from jlab/small_qtp-vis
Small qtp vis
2 parents 826a413 + 6fae6b5 commit 9fb7c51

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‎.github/workflows/buildContainer.yaml‎

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@@ -9,7 +9,7 @@ jobs:
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docker:
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strategy:
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matrix:
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plugin: ["qp-deblur", "qtp-biom", "qp-target-gene", "qtp-sequencing", "nginx"]
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plugin: ["qp-deblur", "qtp-biom", "qp-target-gene", "qtp-sequencing", "nginx", "qtp-visualization"]
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository

‎Images/qtp-visualization/qtp-visualization.dockerfile‎

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FROM ubuntu:24.04
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# VERSION: 2025.08.29
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FROM ubuntu:24.04 AS builder
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ARG MINIFORGE_VERSION=24.1.2-0
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ARG QIIME2RELEASE=2023.5
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ENV CONDA_DIR=/opt/conda
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ENV PATH=${CONDA_DIR}/bin:${PATH}
@@ -29,10 +32,19 @@ RUN conda install tornado
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COPY trigger.py /trigger.py
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# Download qiime2 yaml (make sure to use a qiime2 version that is able to visualize qiime artifacts of the correct version)
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RUN wget --quiet https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml
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RUN wget --quiet https://data.qiime2.org/distro/core/qiime2-${QIIME2RELEASE}-py38-linux-conda.yml
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RUN sed -n '/channels/,/dependencies/p' qiime2-${QIIME2RELEASE}-py38-linux-conda.yml > tinyq2.yml && \
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echo " - q2-metadata=${QIIME2RELEASE}" >> tinyq2.yml && \
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echo " - q2-mystery-stew=${QIIME2RELEASE}" >> tinyq2.yml && \
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echo " - q2-types=${QIIME2RELEASE}" >> tinyq2.yml && \
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echo " - q2cli=${QIIME2RELEASE}" >> tinyq2.yml && \
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echo " - q2templates=${QIIME2RELEASE}" >> tinyq2.yml && \
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echo " - typeguard=2.13.3" >> tinyq2.yml && \
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echo " - qiime2" >> tinyq2.yml
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# Create conda env
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RUN conda env create --name qtp-visualization -y --file qiime2-2023.5-py38-linux-conda.yml
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RUN conda config --set channel_priority strict && conda env create --name qtp-visualization -y --file tinyq2.yml
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# Make RUN commands use the new environment:
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# append --format docker to the build command, see https://github.com/containers/podman/issues/8477
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SHELL ["conda", "run", "-p", "/opt/conda/envs/qtp-visualization", "/bin/bash", "-c"]
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ENV LANG=C.UTF-8
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RUN pip install -U pip
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RUN pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
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RUN pip install https://github.com/qiita-spots/qiita-files/archive/master.zip
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#RUN pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
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RUN git clone -b uncouplePlugins https://github.com/jlab/qiita_client.git
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RUN sed -i "s/f'Entered BaseQiitaPlugin._register_command({command.name})'/'Entered BaseQiitaPlugin._register_command(%s)' % command.name/" qiita_client/qiita_client/plugin.py
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RUN cd qiita_client && pip install --no-cache-dir .
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#RUN pip install https://github.com/qiita-spots/qiita-files/archive/master.zip
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RUN git clone -b master https://github.com/jlab/qiita-files.git
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RUN cd /qiita-files && pip install -e . -v
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RUN git clone https://github.com/qiita-spots/qtp-visualization.git
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WORKDIR qtp-visualization
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WORKDIR /qtp-visualization
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RUN sed -i "s|'qiita_client', 'click >= 3.3', 'qiime2'|'click >= 3.3'|" setup.py
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RUN pip install -e .
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RUN pip install --upgrade certifi
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RUN pip install pip-system-certs
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# TODO: should the plugin get the server configuration?!
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RUN export QIITA_CONFIG_FP=/qiita/config_qiita_oidc.cfg
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WORKDIR /
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RUN repo=q2-metadata; mkdir -p /$repo && wget -O- https://github.com/qiime2/$repo/archive/refs/tags/${QIIME2RELEASE}.0.tar.gz | tar -xz --strip-components=1 -C /$repo
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RUN repo=q2-mystery-stew; mkdir -p /$repo && wget -O- https://github.com/qiime2/$repo/archive/refs/tags/${QIIME2RELEASE}.0.tar.gz | tar -xz --strip-components=1 -C /$repo
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RUN repo=q2-types; mkdir -p /$repo && wget -O- https://github.com/qiime2/$repo/archive/refs/tags/${QIIME2RELEASE}.0.tar.gz | tar -xz --strip-components=1 -C /$repo
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RUN repo=q2cli; mkdir -p /$repo && wget -O- https://github.com/qiime2/$repo/archive/refs/tags/${QIIME2RELEASE}.1.tar.gz | tar -xz --strip-components=1 -C /$repo
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RUN repo=q2templates; mkdir -p /$repo && wget -O- https://github.com/qiime2/$repo/archive/refs/tags/${QIIME2RELEASE}.0.tar.gz | tar -xz --strip-components=1 -C /$repo
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RUN repo=qiime2; mkdir -p /$repo && wget -O- https://github.com/qiime2/$repo/archive/refs/tags/${QIIME2RELEASE}.1.tar.gz | tar -xz --strip-components=1 -C /$repo
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COPY requirements.txt ./requirements.txt
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RUN conda install cython
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RUN pip wheel --no-cache-dir --wheel-dir /wheels -r requirements.txt
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RUN pip install iow
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# ==========================
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# Stage 2: Runtime
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# ==========================
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FROM python:3.8-slim
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# python package compile in build stage
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COPY --from=builder /wheels /wheels
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RUN pip install --no-cache-dir /wheels/* \
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&& rm -rf rm -rf `find /usr/local/lib/python3.8/site-packages -type d -name "tests" | grep -v numpy`
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COPY start_qtp-visualization.sh .
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RUN chmod 755 start_qtp-visualization.sh
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RUN mkdir -p /unshared_plugins
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ENV QIITA_PLUGINS_DIR=/unshared_plugins/
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COPY trigger_noconda.py /trigger.py
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## Export cert and config filepaths
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COPY qiita_server_certificates/qiita_server_certificates.pem /qiita_server_certificates/qiita_server_certificates.pem
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ENV REQUESTS_CA_BUNDLE=/qiita_server_certificates/qiita_server_certificates.pem
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ENV SSL_CERT_FILE=/qiita_server_certificates/qiita_server_certificates.pem
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#RUN export QIITA_ROOTCA_CERT=/unshared_certificates/ci_rootca.crt
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RUN chmod u+x /qtp-visualization/scripts/configure_visualization_types /qtp-visualization/scripts/start_visualization_types
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RUN chmod u+x /usr/local/bin/configure_visualization_types /usr/local/bin/start_visualization_types
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COPY qiita_server_certificates/*_server.* /qiita_server_certificates/
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RUN /qtp-visualization/scripts/configure_visualization_types --env-script "true" --server-cert `find /qiita_server_certificates/ -name "*_server.crt" -type f`
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# qiime2 expects to have a CONDA_PREFIX set, see https://github.com/qiime2/qiime2/blob/812fd09cf80b4ed76c1f39827ae2dba729448436/qiime2/sdk/parallel_config.py#L30
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ENV CONDA_PREFIX=/usr/local
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RUN configure_visualization_types --env-script "true" --server-cert `find /qiita_server_certificates/ -name "*_server.crt" -type f`
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RUN sed -i -E "s/^START_SCRIPT = .+/START_SCRIPT = python \/start_plugin.py qtp-visualization/" /unshared_plugins/*.conf
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CMD ["./start_qtp-visualization.sh"]
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CMD ["./start_qtp-visualization.sh"]

‎Images/qtp-visualization/requirements.txt‎

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-e /q2-metadata
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-e /q2-mystery-stew
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-e /q2-types
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-e /q2cli
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-e /q2templates
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-e /qiime2
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tornado
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pip-system-certs
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pyyaml
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decorator
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tzlocal
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bibtexparser
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psutil
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flufl.lock
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parsl
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appdirs
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tomlkit
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scikit-bio
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rnanorm
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seaborn
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jinja2
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ijson
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pyhmmer
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frictionless
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numpy
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-e /qtp-visualization
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-e /qiita-files
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-e /qiita_client

‎Images/qtp-visualization/start_qtp-visualization.sh‎

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#!/bin/bash
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cd / && python trigger.py qtp-visualization start_visualization_types /qtp-visualization
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cd / && python trigger.py start_visualization_types
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tail -f /dev/null

‎Makefile‎

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$(PODMAN_BIN) build $(TMPDIR)/ -f $(TMPDIR)/`basename $<` $(PODMAN_FLAGS) -t local-`basename $< | cut -d "." -f 1`
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touch .built_image_`basename $< | cut -d "." -f 1`
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.built_image_qtp-visualization: Images/qtp-visualization/qtp-visualization.dockerfile Images/qtp-visualization/start_qtp-visualization.sh
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.built_image_qtp-visualization: Images/qtp-visualization/qtp-visualization.dockerfile Images/qtp-visualization/start_qtp-visualization.sh Images/qtp-visualization/requirements.txt
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tmpdir=$(TMPDIR) $(MAKE) plugin
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cp $^ $(TMPDIR)
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$(PODMAN_BIN) build $(TMPDIR)/ -f $(TMPDIR)/`basename $<` $(PODMAN_FLAGS) -t local-`basename $< | cut -d "." -f 1`

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