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Empiar deposition #17

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Merged
sofyalaski merged 5 commits into from
Jun 5, 2025
Merged

Empiar deposition #17

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0640c92
adding python to docker image to use for pdb_extract and for empiar d…
sofyalaski Apr 22, 2025
c7beee7
wip docker container on mac can't finish up maxit in pdb_extract
sofyalaski May 1, 2025
f339cd7
use pdb_extractor to convert the pdb to cif
sofyalaski Jun 3, 2025
9b561bf
test pdb to cif convertion
sofyalaski Jun 4, 2025
0652164
fix linting errors
sofyalaski Jun 5, 2025
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6 changes: 3 additions & 3 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -397,8 +397,8 @@ FodyWeavers.xsd
# JetBrains Rider
*.sln.iml


.vscode/
bearer.jwt
dist/
mmcif_pdbx_v50.dic
conversions.csv
# mmcif_pdbx_v50.dic
# conversions.csv
63 changes: 49 additions & 14 deletions Dockerfile
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@@ -1,7 +1,7 @@
# syntax=docker/dockerfile:1

# Build stage
FROM golang:1.22 AS builder
FROM golang:1.23 AS builder

# Set destination for COPY
WORKDIR /app
Expand All @@ -12,32 +12,67 @@ RUN go mod download

# Copy the source code
COPY main.go ./
COPY conversions.csv /app/conversions.csv
COPY mmcif_pdbx_v50.dic /app/mmcif_pdbx_v50.dic
COPY /data/conversions.csv /app/data/conversions.csv
COPY /data/mmcif_pdbx_v50.dic /app/data/mmcif_pdbx_v50.dic
COPY depositions/onedep ./depositions/onedep
COPY docs ./docs
COPY README.md /app/README.md
COPY /data/empiar_deposition.schema.json /app/data/empiar_deposition.schema.json

ARG VERSION=v.0.1.0

# Build GOARCH=amd64
RUN CGO_ENABLED=0 GOOS=linux GOARCH=${TARGETARCH} go generate .
RUN CGO_ENABLED=0 GOOS=linux GOARCH=${TARGETARCH} go build -o /app/depositor

# Final stage
FROM alpine:latest
# Stage 2: download pdb_extract
FROM alpine:3.20 AS extractor

# Set environment variables
ENV PORT=8888
ENV ALLOW_ORIGINS=http://localhost:4200
WORKDIR /opt/pdb_extract

# Copy the binary and other necessary files from the builder stage
RUN apk add --no-cache curl tar
RUN VERSION=$(curl -s https://sw-tools.rcsb.org/apps/PDB_EXTRACT/pdb-extract-latest-version.txt) && \
curl -LO https://sw-tools.rcsb.org/apps/PDB_EXTRACT/pdb_extract_prod_py-${VERSION}.tar.gz && \
tar -xzf pdb_extract_prod_py-${VERSION}.tar.gz

# Final stage using slim because maxit is incompatible with alpine
FROM python:3.12-slim AS final

WORKDIR /app

# Install system dependencies
RUN apt-get update && apt-get install -y \
bash \
curl \
build-essential \
cmake \
flex \
bison \
&& rm -rf /var/lib/apt/lists/*

# Copy Go app
COPY --from=builder /app/depositor /app/depositor
COPY --from=builder /app/conversions.csv /app/conversions.csv
COPY --from=builder /app/mmcif_pdbx_v50.dic /app/mmcif_pdbx_v50.dic
COPY --from=builder /app/data/conversions.csv /app/data/conversions.csv
COPY --from=builder /app/data/mmcif_pdbx_v50.dic /app/data/mmcif_pdbx_v50.dic
COPY --from=builder /app/README.md /app/README.md
#WILL REMOVE LATER
COPY --from=builder /app/data/empiar_deposition.schema.json /app/data/empiar_deposition.schema.json
# Copy extracted pdb_extract directory
COPY --from=extractor /opt/pdb_extract/pdb_extract_prod_py-* /app/scripts/


# Set up pdb_extract environment
WORKDIR /app/scripts
RUN pip install --upgrade pip && \
pip install -r REQUIREMENTS.txt && \
bash install.sh

EXPOSE 8888
# Run
WORKDIR /app
CMD ["./depositor"]

ENV PORT=8080
ENV ALLOW_ORIGINS=http://localhost:4201
ENV RCSBROOT=/app/scripts/packages/maxit-v11.300-prod-src

EXPOSE 8080

CMD ["./depositor"]
0 conversions.csv → data/conversions.csv
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