saalfeldlab · sukeshsangam · Dec 17, 2021 · Dec 17, 2021 · Dec 17, 2021 · Dec 17, 2021
diff --git a/Dockerfile b/Dockerfile
@@ -33,7 +33,7 @@ COPY . /var/www/render/
 RUN mvn clean
 
 # use -T 1C option to multi-thread maven, using 1 thread per available core
-RUN mvn -T 1C -Dproject.build.sourceEncoding=UTF-8 package && \
+RUN mvn -T 1C -Dproject.build.sourceEncoding=UTF-8 -Dmaven.test.skip=true package && \
     mkdir -p /root/render-lib && \
     mv */target/*.*ar /root/render-lib && \
     printf "\nsaved the following build artifacts:\n\n" && \
@@ -49,13 +49,13 @@ RUN mvn -T 1C -Dproject.build.sourceEncoding=UTF-8 package && \
 # Once web service application is built, set up jetty server and deploy application to it.
 
 # NOTE: jetty version should be kept in sync with values in render/render-ws/pom.xml and render/render-ws/src/main/scripts/install.sh
-FROM jetty:9.4.43-jdk8-slim as render-ws
+FROM jetty:9.4.9-jre8-alpine as render-ws
 
 # add packages not included in alpine:
 #   curl and coreutils for gnu readlink
 #   fontconfig and ttf-dejavu for bounding box renderer ( see https://github.com/docker-library/openjdk/pull/202 )
 USER root
-RUN apt-get update && apt-get install -y curl coreutils fontconfig ttf-dejavu
+RUN apk add --no-cache curl coreutils fontconfig ttf-dejavu
 
 WORKDIR $JETTY_BASE
 
@@ -69,10 +69,10 @@ RUN ls -al $JETTY_BASE/* && \
 COPY --from=builder /root/render-lib/render-ws-*.war webapps/render-ws.war
 COPY render-ws/src/main/scripts/docker /render-docker
 RUN chown -R jetty:jetty $JETTY_BASE 
-
+RUN chmod -R 777 $JETTY_BASE
 EXPOSE 8080
 
-ENV JAVA_OPTIONS="-Xms3g -Xmx3g -server -Djava.awt.headless=true" \
+ENV JAVA_OPTIONS="-Xms45g -Xmx45g -server -Djava.awt.headless=true" \
     JETTY_THREADPOOL_MIN_THREADS="10" \
     JETTY_THREADPOOL_MAX_THREADS="200" \
     LOG_ACCESS_ROOT_APPENDER="STDOUT" \
@@ -89,6 +89,12 @@ ENV JAVA_OPTIONS="-Xms3g -Xmx3g -server -Djava.awt.headless=true" \
     NDVIZHOST="" \
     NDVIZPORT="" \
     NDVIZ_URL="" \
+    VIEW_OPENSEADRAGON_HOST_AND_PORT="" \
+    VIEW_DATA_PREP="" \
+    VIEW_DATA_PREPSH="" \
+    VIEW_OPENSEADRAGON_DATA_HOST="" \
+    VIEW_OPENSEADRAGON_DATA_SOURCE_FOLDER="" \
+    VIEW_OPENSEADRAGON_DATA_DESTINATION_FOLDER="" \
     VIEW_CATMAID_HOST_AND_PORT="" \
     VIEW_DYNAMIC_RENDER_HOST_AND_PORT="" \
     VIEW_RENDER_STACK_OWNER="" \

diff --git a/README.md b/README.md
@@ -18,4 +18,42 @@ A collection of Java tools and HTTP services (APIs) for rendering transformed im
   [render application]: <docs/src/site/markdown/render-app.md>
   [render web services]: <docs/src/site/markdown/render-ws.md>
   [RESTful APIs]: <docs/src/site/markdown/render-ws-api/render-ws-api.md>
-  [Docker packaging]: <docs/src/site/markdown/render-ws-docker.md>
+  [Docker packaging]: <docs/src/site/markdown/render-ws-docker.md>
+
+
+# Openseadragon Viewer for Render service:
+
+  In this branch Openseadragon Viewer feature is developed for the Render Service. 
+
+  Openseadragon is a web-based viewer for high resolution zoomable images implemented in Javascript. To know more about it please refer (https://openseadragon.github.io/)
+
+  In this branch Rendered images are converted to Deep Zoom images to feed into openseadragon viewer. 
+
+  MagickSlicer is used to convert the rendered images to DZI(Deep Zoom Images) (https://github.com/VoidVolker/MagickSlicer)
+
+  The Rendered images and the converted DZI images are stored on a http server, which are used by openseadragon viewer.
+
+  A python script is used to run the DZI image convertion pipeline on the HPC cluster. This python script needs to be placed on HPC Cluster and 
+  the file path should be provided as the parameter in the Dockerfile.
+
+  Here are the parameters which should be provided in Dockerfile to enable openseadragon viewer feature.
+
+  VIEW_OPENSEADRAGON_HOST_AND_PORT=""  (render-ws/src/main/webapp/view/openseadragon.html file web URL)
+  VIEW_DATA_PREP="" \ (python file Path on the HPC cluster, openseadragon/derived_data_preparation_code/data_preparation.py)
+  VIEW_DATA_PREPSH="" \ (magick-slicer shell script path which is placed on HPC cluster, https://github.com/VoidVolker/MagickSlicer)
+  VIEW_OPENSEADRAGON_DATA_HOST="" \ (HTTP webserver where the rendered and DZI images are placed)
+  VIEW_OPENSEADRAGON_DATA_SOURCE_FOLDER="" \ (rendered images path on HPC cluster or http webserver link)
+  VIEW_OPENSEADRAGON_DATA_DESTINATION_FOLDER="" \ (Destination folder PATH on the HPC cluster)
+
+
+  In this branch, there is feature where you can submit a job to the cluster to convert rendered images to DZI images, cluster details and credentials can be provided through the user interface in stacks.html page.
+
+  you can view the DZI images of the stacks in the openseadragon viewer by clicking on 'view in openseadragon' hyperlink in the stacks section.
+
+
+
+
+
+
+
+
diff --git a/docs/docs.iml b/docs/docs.iml
diff --git a/docs/pom.xml b/docs/pom.xml
@@ -54,7 +54,7 @@
       Administrative elements required by org.scijava.maven.plugin.enforcer.RequireElements
       that have to be copied.  Too bad they can't just be taken from parent pom.
     -->
-    <url>https://github.com/saalfeldlab/render</url>
+    <url>https://github.com/sukeshsangam/render</url>
     <inceptionYear>2014</inceptionYear>
     <organization><name>see parent</name></organization>
     <licenses><license><name>see parent</name></license></licenses>
@@ -69,4 +69,4 @@
         <license.copyrightOwners>Howard Hughes Medical Institute</license.copyrightOwners>
     </properties>
 
-</project>
+</project>
diff --git a/openseadragon/derived_data_preparation_code/.data_preparation.py.swp b/openseadragon/derived_data_preparation_code/.data_preparation.py.swp
diff --git a/openseadragon/derived_data_preparation_code/MagickSlicer b/openseadragon/derived_data_preparation_code/MagickSlicer
diff --git a/openseadragon/derived_data_preparation_code/data_preparation.py b/openseadragon/derived_data_preparation_code/data_preparation.py
@@ -0,0 +1,24 @@
+import urllib.request
+import sys
+import json
+import os
+import smtplib
+from pathlib import Path
+response = urllib.request.urlopen('http://'+sys.argv[9]+'/render-ws/v1/owner/'+sys.argv[1]+'/project/'+sys.argv[2]+'/stack/'+sys.argv[3]+'/bounds')
+data_json=json.loads(response.read())
+width=int(data_json['maxX']-data_json['minX'])
+height=int(data_json['maxY']-data_json['minY'])
+X=data_json['minX']
+Y=data_json['minY']
+minZ=data_json['minZ']
+maxZ=data_json['maxZ']
+#os.system("pip3 install pymongo")
+#os.system("pip3 install dnspython")
+for z in range(int(minZ),int(maxZ+1)):
+        source_folder=sys.argv[8]+sys.argv[1]+"/"+sys.argv[2]+"/"+sys.argv[3]
+        Path(source_folder).mkdir(parents=True, exist_ok=True)
+        urllib.request.urlretrieve("http://"+sys.argv[9]+"/render-ws/v1/owner/"+sys.argv[1]+"/project/"+sys.argv[2]+"/stack/"+sys.argv[3]+"/z/"+str(z)+"/box/"+str(X)+","+str(Y)+","+str(width)+","+str(height)+",1/jpeg-image?scale=1", source_folder+"/"+sys.argv[1]+"_"+sys.argv[2]+"_"+sys.argv[3]+"_"+str(z)+".jpg")
+        destination_folder=sys.argv[6]+sys.argv[1]+"/"+sys.argv[2]+"/"+sys.argv[3]+"/"+sys.argv[1]+"_"+sys.argv[2]+"_"+sys.argv[3]+"_"+str(z)+".jpg"
+        Path(destination_folder).mkdir(parents=True, exist_ok=True)
+        os.system(sys.argv[5]+" "+source_folder+"/"+sys.argv[1]+"_"+sys.argv[2]+"_"+sys.argv[3]+"_"+str(z)+".jpg"+" "+destination_folder)
+
diff --git a/pom.xml b/pom.xml
@@ -16,7 +16,7 @@
     <version>2.3.0</version>
 
     <description>A collection of tools and HTTP services (APIs) for rendering transformed image tiles.</description>
-    <url>https://github.com/saalfeldlab/render</url>
+    <url>https://github.com/sukeshsangam/render.git</url>
     <inceptionYear>2014</inceptionYear>
     <organization>
         <name>Janelia Research Campus</name>
@@ -79,7 +79,7 @@
     </mailingLists>
 
     <scm>
-        <url>https://github.com/saalfeldlab/render</url>
+        <url>https://github.com/sukeshsangam/render.git</url>
     </scm>
 
     <issueManagement>

diff --git a/render-app/pom.xml b/render-app/pom.xml
@@ -131,7 +131,7 @@
       Administrative elements required by org.scijava.maven.plugin.enforcer.RequireElements
       that have to be copied.  Too bad they can't just be taken from parent pom.
     -->
-    <url>https://github.com/saalfeldlab/render</url>
+    <url>https://github.com/sukeshsangam/render</url>
     <inceptionYear>2014</inceptionYear>
     <organization><name>see parent</name></organization>
     <licenses><license><name>see parent</name></license></licenses>

diff --git a/render-app/render-app.iml b/render-app/render-app.iml
diff --git a/render-ws-java-client/pom.xml b/render-ws-java-client/pom.xml
@@ -124,7 +124,7 @@
       Administrative elements required by org.scijava.maven.plugin.enforcer.RequireElements
       that have to be copied.  Too bad they can't just be taken from parent pom.
     -->
-    <url>https://github.com/saalfeldlab/render</url>
+    <url>https://github.com/sukeshsangam/render</url>
     <inceptionYear>2014</inceptionYear>
     <organization><name>see parent</name></organization>
     <licenses><license><name>see parent</name></license></licenses>