feat: support upcoming server version 22.0.0

* Adds compatibility with sample responses with no `caches` field.
* Resolves `pyyaml` packaging issues

Dockerfile

@@ -1,40 +1,68 @@
-FROM python:3.10-buster as spades
+FROM debian:buster as prep
 WORKDIR /build
+RUN apt-get update && apt-get install -y cmake gcc g++ make unzip wget zlib1g-dev
+RUN wget https://zlib.net/pigz/pigz-2.8.tar.gz
+RUN tar -xvf pigz-2.8.tar.gz
+WORKDIR /build/pigz-2.8
+RUN make
+WORKDIR /build
+RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
+RUN unzip fastqc_v0.11.9.zip
+RUN wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.2/bowtie2-2.3.2-legacy-linux-x86_64.zip
+RUN unzip bowtie2-2.3.2-legacy-linux-x86_64.zip
+RUN mkdir bowtie2
+RUN cp bowtie2-2.3.2-legacy/bowtie2* bowtie2
 RUN wget https://github.com/ablab/spades/releases/download/v3.11.0/SPAdes-3.11.0-Linux.tar.gz
 RUN tar -xvf SPAdes-3.11.0-Linux.tar.gz
 RUN mv SPAdes-3.11.0-Linux spades
 RUN sed -i 's/import collections/import collections\nimport collections.abc/g' spades/share/spades/pyyaml3/constructor.py
 RUN sed -i 's/key, collections.Hashable/key, collections.abc.Hashable/g' spades/share/spades/pyyaml3/constructor.py
-
-FROM python:3.10-buster as rust
+RUN wget http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz
+RUN tar -xf hmmer-3.2.1.tar.gz
+WORKDIR /build/hmmer-3.2.1
+RUN ./configure --prefix /build/hmmer
+RUN make
+RUN make install
 WORKDIR /build
+RUN wget https://github.com/relipmoc/skewer/archive/0.2.2.tar.gz
+RUN tar -xf 0.2.2.tar.gz
+WORKDIR /build/skewer-0.2.2
+RUN make
+RUN mv skewer /build
+
+FROM python:3.10-buster as base
+WORKDIR /app
+COPY --from=prep /build/bowtie2/* /usr/local/bin/
+COPY --from=prep /build/FastQC /opt/fastqc
+COPY --from=prep /build/hmmer /opt/hmmer
+COPY --from=prep /build/pigz-2.8/pigz /usr/local/bin/pigz
+COPY --from=prep /build/skewer /usr/local/bin/
+COPY --from=prep /build/spades /opt/spades
+RUN chmod ugo+x /opt/fastqc/fastqc && \
+    ln -fs /opt/fastqc/fastqc /usr/local/bin/fastqc && \
+    for file in `ls /opt/hmmer/bin`; do ln -fs /opt/hmmer/bin/${file} /usr/local/bin/${file};  done
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends curl build-essential default-jre && \
+    rm -rf /var/lib/apt/lists/* && \
+    apt-get clean
 RUN apt-get update && apt-get install -y curl build-essential
 RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
-ENV PATH="/root/.cargo/bin:${PATH}"
+RUN curl -sSL https://install.python-poetry.org | python -
+ENV PATH="/root/.cargo/bin:/root/.local/bin:/opt/spades/bin:${PATH}"
+RUN pip install --upgrade pip
 RUN pip install maturin==0.14.12
 COPY src src
-COPY Cargo.toml Cargo.lock pyproject.toml ./
+COPY Cargo.toml Cargo.lock poetry.lock pyproject.toml workflow.py ./
 RUN maturin build --release
+RUN poetry export > requirements.txt
+RUN pip install -r requirements.txt
+RUN pip install /app/target/wheels/nuvs_rust*.whl
 
-FROM python:3.10-buster as pip
-RUN pip install --upgrade pip
-RUN pip install --user biopython
-COPY --from=rust /build/target/wheels/nuvs_rust*.whl ./
-RUN pip install --user nuvs_rust*.whl
-
-FROM virtool/workflow:5.2.1 as test
-WORKDIR /workflow
-COPY --from=spades /build/spades /opt/spades
+FROM base as test
+WORKDIR /app
 ENV PATH="/opt/spades/bin:${PATH}"
-COPY --from=pip /root/.local /root/.local
-COPY workflow.py /workflow/workflow.py
-RUN pip install --user pytest pytest-asyncio==0.15.1 pytest-aiohttp==0.3.0 pytest-regressions pydantic-factories pytest-rerunfailures
+RUN poetry export --with dev > requirements.txt
+RUN pip install -r requirements.txt
+COPY workflow.py ./
 COPY tests ./tests
-ENTRYPOINT ["pytest"]
-
-FROM virtool/workflow:5.3.0 as base
-WORKDIR /workflow
-COPY --from=spades /build/spades /opt/spades
-ENV PATH="/opt/spades/bin:${PATH}"
-COPY --from=pip /root/.local /root/.local
-COPY workflow.py /workflow/workflow.py
+RUN pytest