Merge pull request #613 from populationgenomics/dev

Release
populationgenomics · Nov 15, 2023 · e8025df · e8025df
2 parents f222398 + c05b11e
commit e8025df
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Showing 3 changed files with 454 additions and 15 deletions.
diff --git a/deploy/api/Dockerfile b/deploy/api/Dockerfile
@@ -1,9 +1,7 @@
-FROM debian:buster-slim
+FROM python:3.11
 
 ARG SM_ENVIRONMENT
 
-ENV MAMBA_ROOT_PREFIX /root/micromamba
-ENV PATH $MAMBA_ROOT_PREFIX/bin:$PATH
 ENV PORT 8000
 ENV SM_ENVIRONMENT ${SM_ENVIRONMENT}
 # Allow statements and log messages to immediately appear in the Knative logs.
@@ -14,15 +12,7 @@ EXPOSE $PORT
 WORKDIR /app/sample_metadata/
 COPY requirements.txt requirements.txt
 
-RUN apt-get update && \
-    apt-get install -y wget bash bzip2 zip build-essential && \
-    rm -r /var/lib/apt/lists/* /var/cache/apt/* && \
-    wget -qO- https://api.anaconda.org/download/conda-forge/micromamba/0.8.2/linux-64/micromamba-0.8.2-he9b6cbd_0.tar.bz2 | tar -xvj -C /usr/local bin/micromamba && \
-    mkdir $MAMBA_ROOT_PREFIX && \
-    micromamba install -y --prefix $MAMBA_ROOT_PREFIX -c conda-forge \
-        python=3.10 pip && \
-    pip install -r requirements.txt && \
-    rm -r /root/micromamba/pkgs
+RUN pip install --no-cache-dir -r requirements.txt
 
 COPY api api
 COPY db db/

diff --git a/scripts/create_test_subset.py b/scripts/create_test_subset.py
@@ -32,7 +32,6 @@
     SequencingGroupUpsert,
 )
 
-
 logger = logging.getLogger(__file__)
 logging.basicConfig(format='%(levelname)s (%(name)s %(lineno)s): %(message)s')
 logger.setLevel(logging.INFO)
@@ -385,7 +384,7 @@ def transfer_analyses(
                             project,
                             (str(sg['id']), new_sg_map[s['externalId']][0]),
                         ),
-                        status=AnalysisStatus(analysis['status'].lower()),
+                        status=AnalysisStatus(analysis['status'].lower().replace('_', '-')),
                         sequencing_group_ids=new_sg_map[s['externalId']],
                         meta=analysis['meta'],
                     )
@@ -401,7 +400,7 @@ def transfer_analyses(
                             project,
                             (str(sg['id']), new_sg_map[s['externalId']][0]),
                         ),
-                        status=AnalysisStatus(analysis['status'].lower()),
+                        status=AnalysisStatus(analysis['status'].lower().replace('_', '-')),
                         sequencing_group_ids=new_sg_map[s['externalId']],
                         meta=analysis['meta'],
                     )