fix: improve error visibility

* Try to improve quality of errors reported to Sentry.
* Log exceptions that are pushed to the API in error status reports.
* Extend tracebacks reported to API.
* Fix broken image build.

Author: igboyes

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
       - name: Build
-        run: docker build .
+        run: docker build --target=base .
   test:
     runs-on: ubuntu-22.04
     steps:

Dockerfile

@@ -1,31 +1,45 @@
-FROM python:3.10-buster as rust_utils
+FROM debian:buster as prep
 WORKDIR /build
-RUN apt-get update && apt-get install -y curl build-essential
+RUN apt-get update && apt-get install -y make gcc zlib1g-dev wget unzip
+RUN wget https://zlib.net/pigz/pigz-2.7.tar.gz && \
+    tar -xzvf pigz-2.7.tar.gz && \
+    cd pigz-2.7 && \
+    make
+RUN wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip && \
+    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 && \
+    unzip bowtie2-2.3.2-legacy-linux-x86_64.zip && \
+    mkdir bowtie2 && \
+    cp bowtie2-2.3.2-legacy/bowtie2* bowtie2
+
+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/pigz-2.7/pigz /usr/local/bin/pigz
+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 curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
-ENV PATH="/root/.cargo/bin:${PATH}"
+RUN curl -sSL https://install.python-poetry.org | python -
+ENV PATH="/root/.cargo/bin:/root/.local/bin:${PATH}"
+RUN pip install --upgrade pip
 RUN pip install maturin==0.14.5
 COPY src src
-COPY Cargo.toml Cargo.lock ./
+COPY Cargo.toml Cargo.lock fixtures.py pathoscope.py  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/rust_utils*.whl
 
-FROM virtool/workflow:5.3.0 as base
-WORKDIR /app
-RUN pip install --upgrade pip
-COPY fixtures.py workflow.py pathoscope.py ./
-COPY --from=rust_utils /build/target/wheels/rust_utils*.whl ./
-RUN ls
-RUN pip install rust_utils*.whl
 
-FROM virtool/workflow:5.3.0 as test
-WORKDIR /test
-RUN pip install --upgrade pip
-COPY pyproject.toml poetry.lock ./
-RUN curl -sSL https://install.python-poetry.org | python -
-COPY tests /test/tests
-COPY fixtures.py workflow.py pathoscope.py ./
-COPY --from=rust_utils /build/target/wheels/rust_utils*.whl ./
-RUN pip install rust_utils*.whl
-RUN poetry install
-RUN poetry add ./rust_utils*.whl
-RUN ls
-RUN poetry run pytest
+FROM base as test
+WORKDIR /app
+RUN poetry export  --with dev > requirements.txt
+RUN pip install -r requirements.txt
+COPY tests ./tests
+RUN pytest

poetry.lock

@@ -7,7 +7,7 @@ license = "MIT"
 
 [tool.poetry.dependencies]
 python = "~3.10"
-virtool-workflow = "^5.0.0"
+virtool-workflow = "^5.3.1"
 rust = "^0.1.1"
 
 [tool.poetry.group.dev.dependencies]

pyproject.toml

@@ -125,14 +125,8 @@ class SubtractionFactory(ModelFactory):
             **{**_subtraction1.dict(), "ready": True},
             path=subtraction_path,
         ),
-        WFSubtraction(
-            **{**_subtraction2.dict(), "ready": True},
-            path=subtraction_path
-        ),
-        WFSubtraction(
-            **{**_subtraction3.dict(), "ready": True},
-            path=subtraction_path
-        )
+        WFSubtraction(**{**_subtraction2.dict(), "ready": True}, path=subtraction_path),
+        WFSubtraction(**{**_subtraction3.dict(), "ready": True}, path=subtraction_path),
     ]
 
 
@@ -194,7 +188,9 @@ async def test_map_isolates(
 
 
 @pytest.mark.datafiles(SAM_PATH, FASTQ_PATH)
-async def test_eliminate_subtraction(datafiles, subtractions, work_path, run_subprocess):
+async def test_eliminate_subtraction(
+    datafiles, subtractions, work_path, run_subprocess
+):
     isolate_fastq_path = work_path / "test.fq"
     isolate_sam_path = work_path / "test_al.sam"