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fix: update docker build process #129

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Merged
sameeul merged 1 commit into from
Feb 17, 2026
Merged

fix: update docker build process #129

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13 changes: 10 additions & 3 deletions docker/base/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -58,11 +58,12 @@ RUN mkdir -p /usr/share/maven/conf && \
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' \
'xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 ' \
'http://maven.apache.org/xsd/settings-1.0.0.xsd">' \
'<localRepository>/etc/m2</localRepository>' \
'<localRepository>/etc/m2/repository</localRepository>' \
'</settings>' > /usr/share/maven/conf/settings.xml

# Ensure the /etc/m2 directory exists
RUN mkdir -p /etc/m2
# Ensure the /etc/m2 directory and subdirectories exist
RUN mkdir -p /etc/m2/repository
RUN mkdir -p /etc/m2/jgo_cache

# Set the correct permissions
RUN chmod -R 777 ${EXEC_DIR} && \
Expand All @@ -71,5 +72,11 @@ RUN chmod -R 777 ${EXEC_DIR} && \

RUN python3 -c 'import bfio; bfio.start()'

# Verify that the JAR file exists somewhere within /etc/m2
RUN echo "Verifying JAR files in /etc/m2:" && \
find /etc/m2 -name "formats-gpl-8.0.1.jar" -exec ls -lh {} \; && \
echo "All JAR files in /etc/m2:" && \
find /etc/m2 -name "*.jar" | head -20

# Set the correct permissions again, for sanity
RUN chmod -R 777 /etc/m2
17 changes: 11 additions & 6 deletions docker/imagej/Dockerfile
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Expand Up @@ -38,9 +38,6 @@ RUN python3 -m pip install --upgrade pip --no-cache-dir
# Copy the source
COPY . /bfio_src

# Apply m2 repo patch
RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch

# Install
RUN python3 -m pip install /bfio_src --no-cache-dir

Expand All @@ -64,19 +61,27 @@ RUN mkdir -p /usr/share/maven/conf && \
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" \
xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 \
http://maven.apache.org/xsd/settings-1.0.0.xsd"> \
<localRepository>/etc/m2</localRepository> \
<localRepository>/etc/m2/repository</localRepository> \
</settings>' \
> /usr/share/maven/conf/settings.xml

# Ensure the /etc/m2 directory exists
RUN mkdir -p /etc/m2
# Ensure the /etc/m2 directory and subdirectories exist
RUN mkdir -p /etc/m2/repository
RUN mkdir -p /etc/m2/jgo_cache

# Set the correct permissions
RUN chmod -R 777 ${EXEC_DIR} && \
chmod -R 777 ${DATA_DIR} && \
chmod -R 777 /etc/m2

RUN python3 -c 'import bfio; bfio.start()'

# Verify that the JAR file exists somewhere within /etc/m2
RUN echo "Verifying JAR files in /etc/m2:" && \
find /etc/m2 -name "formats-gpl-8.0.1.jar" -exec ls -lh {} \; && \
echo "First 10 JAR files in /etc/m2:" && \
find /etc/m2 -name "*.jar" | head -10

RUN python3 -c 'import imagej; ij = imagej.init(); print(ij.getVersion())'

# Set the correct permissions again, for sanity
Expand Down
13 changes: 0 additions & 13 deletions docker/jgo_copy.patch
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This file was deleted.

5 changes: 2 additions & 3 deletions docker/m2_repo.patch
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,10 @@ diff --git a/src/bfio/utils.py b/src/bfio/utils.py
index 954d682..cb88332 100644
--- a/src/bfio/utils.py
+++ b/src/bfio/utils.py
@@ -40,6 +40,8 @@ try:
@@ -40,6 +40,7 @@ try:

global JAR_VERSION
scyjava.config.endpoints.append("ome:formats-gpl:8.0.1")
+ scyjava.config.set_m2_repo("/etc/m2/")
+ scyjava.config.set_cache_dir("/etc/m2/jgo_cache")
scyjava.start_jvm()
import loci
Expand Down
4 changes: 2 additions & 2 deletions docker/pyimagej_m2repo.patch
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Expand Up @@ -4,9 +4,9 @@ index 18aa9a8..74524ce 100644
+++ b/imagej/__init__.py
@@ -1421,6 +1421,7 @@ def _create_jvm(
sj.config.endpoints.extend(original_endpoints)

try:
+ sj.config.set_m2_repo("/etc/m2/")
+ sj.config.set_cache_dir("/etc/m2/jgo_cache")
sj.start_jvm()
except subprocess.CalledProcessError as e:
# Check to see if initialization failed due to "un-managed"
13 changes: 10 additions & 3 deletions docker/tensorflow/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -46,11 +46,12 @@ RUN echo '<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0" ' \
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' \
'xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 ' \
'http://maven.apache.org/xsd/settings-1.0.0.xsd">' \
'<localRepository>/etc/m2</localRepository>' \
'<localRepository>/etc/m2/repository</localRepository>' \
'</settings>' > /usr/share/maven/conf/settings.xml

# Ensure the /etc/m2 directory exists
RUN mkdir -p /etc/m2
# Ensure the /etc/m2 directory and subdirectories exist
RUN mkdir -p /etc/m2/repository
RUN mkdir -p /etc/m2/jgo_cache

# Set the correct permissions
RUN chmod -R 777 ${EXEC_DIR} && \
Expand All @@ -59,5 +60,11 @@ RUN chmod -R 777 ${EXEC_DIR} && \

RUN python3 -c 'import bfio; bfio.start()'

# Verify that the JAR file exists somewhere within /etc/m2
RUN echo "Verifying JAR files in /etc/m2:" && \
find /etc/m2 -name "formats-gpl-8.0.1.jar" -exec ls -lh {} \; && \
echo "First 10 JAR files in /etc/m2:" && \
find /etc/m2 -name "*.jar" | head -10

# Set the correct permissions again, for sanity
RUN chmod -R 777 /etc/m2