add jgo, pyimage patch and update docker files

PolusAI · Jul 19, 2024 · 37b9454 · 37b9454
1 parent f785f77
commit 37b9454
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Showing 5 changed files with 50 additions and 6 deletions.
diff --git a/docker/base/Dockerfile b/docker/base/Dockerfile
@@ -31,8 +31,14 @@ COPY . /bfio_src
 RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch
 
 # Install
-RUN pip3 install /bfio_src --no-cache-dir && \
-    rm -rf /bfio_src
+RUN pip3 install /bfio_src --no-cache-dir
+
+#Apply jgo copy patch
+RUN  git apply  --directory=usr/local/lib/python3.10/dist-packages /bfio_src/docker/jgo_copy.patch
+
+# clean up
+RUN rm -rf /bfio_src
+
 
 # Update Maven local repository path
 RUN mkdir -p /usr/share/maven/conf

diff --git a/docker/imagej/Dockerfile b/docker/imagej/Dockerfile
@@ -37,14 +37,22 @@ COPY . /bfio_src
 RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch
 
 # Install
-RUN pip3 install /bfio_src --no-cache-dir && \
-    rm -rf /bfio_src
+RUN pip3 install /bfio_src --no-cache-dir
+
+#Apply jgo copy patch
+RUN  git apply  --directory=usr/local/lib/python3.9/dist-packages /bfio_src/docker/jgo_copy.patch
 
 # Install packages
 ENV LIBRARY_PATH=/lib:/usr/lib
 RUN pip3 install cython --no-cache-dir && \
     pip3 install pyimagej==1.4.1 --no-cache-dir
 
+#Apply pyimagej patch
+RUN  git apply  --directory=usr/local/lib/python3.9/dist-packages /bfio_src/docker/pyimagej_m2repo.patch
+
+# clean up
+RUN rm -rf /bfio_src
+
 # Update Maven local repository path
 RUN mkdir -p /usr/share/maven/conf
 RUN echo '<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0" ' \

diff --git a/docker/jgo_copy.patch b/docker/jgo_copy.patch
@@ -0,0 +1,13 @@
+diff --git a/jgo/jgo.py b/jgo/jgo.py
+index bd2b328..e2a824a 100644
+--- a/jgo/jgo.py
++++ b/jgo/jgo.py
+@@ -710,7 +710,7 @@ def resolve_dependencies(
+                     jar_file_in_workspace,
+                     link_type=link_type,
+                 )
+-            except FileExistsError:
++            except (FileExistsError, shutil.SameFileError):
+                 # Do not throw exception if target file exists.
+                 pass
+     pathlib.Path(build_success_file).touch(exist_ok=True)
diff --git a/docker/pyimagej_m2repo.patch b/docker/pyimagej_m2repo.patch
@@ -0,0 +1,12 @@
+diff --git a/imagej/__init__.py b/imagej/__init__.py
+index 18aa9a8..74524ce 100644
+--- a/imagej/__init__.py
++++ 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.start_jvm()
+     except subprocess.CalledProcessError as e:
+         # Check to see if initialization failed due to "un-managed"
diff --git a/docker/tensorflow/Dockerfile b/docker/tensorflow/Dockerfile
@@ -32,8 +32,13 @@ COPY . /bfio_src
 RUN git apply --directory=bfio_src /bfio_src/docker/m2_repo.patch
 
 # Install
-RUN pip3 install /bfio_src --no-cache-dir && \
-    rm -rf /bfio_src
+RUN pip3 install /bfio_src --no-cache-dir
+
+#Apply jgo copy patch
+RUN  git apply  --directory=usr/local/lib/python3.8/dist-packages /bfio_src/docker/jgo_copy.patch
+
+# clean up
+RUN rm -rf /bfio_src
 
 # Update Maven local repository path
 RUN mkdir -p /usr/share/maven/conf