Merge branch 'index-instead-jpa'

# Conflicts:
#	pom.xml

.github/workflows/maven.yml

@@ -15,13 +15,13 @@ jobs:
   build:
     runs-on: ubuntu-latest
     env:
-      _JAVA_OPTIONS: "--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.lang.reflect=ALL-UNNAMED"
+      JDK_JAVA_OPTIONS: "--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 20
           distribution: 'temurin'
           cache: maven
-      - name: Build with Maven and JDK-17
+      - name: Build with Maven and JDK-20
         run: mvn --batch-mode --update-snapshots package

Dockerfile

@@ -1,15 +1,17 @@
-# builds the image after maven build from local sources
-# todo: test (perhaps get the data from PC2 and the fat JAR/WAR from M2 repo instead of using local build)
-FROM openjdk:17
-ARG WRK=target/work
-VOLUME /work
-WORKDIR /work
-COPY target/cpath2.war .
-# copy the data except listed in .dockerignore
-COPY $WRK .
+FROM eclipse-temurin:latest
+ARG APP_JAR
+# persistent volume containing the app data (biopax model ad index files;
+# can use target/work demo/test data)
+COPY ${APP_JAR} cpath2.war
+#home/work dir (properties, data) to mount as docker volume/bind (with e.g. terraform or docker-compose)
 ENV CPATH2_HOME /work
-ENTRYPOINT ["java", "-Djava.security.egd=file:/dev/./urandom", "-Dfile.encoding=UTF-8", "-Xmx64g",\
-"-Dspring.profiles.active=docker", "-jar", "cpath2.war", "--server", \
-"--add-opens=java.base/java.lang=ALL-UNNAMED", \
-"--add-opens=java.base/java.lang.reflect=ALL-UNNAMED"]
+ENV JDK_JAVA_OPTIONS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED --add-opens java.base/sun.nio.ch=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED"
+#start the app in the workdir to use the "production" application.properties (if present)
+WORKDIR ${CPATH2_HOME}
+ENTRYPOINT ["java", "-server", "-Djava.security.egd=file:/dev/./urandom", \
+"-Dfile.encoding=UTF-8", "-Xss32m", "-Xmx64g", \
+"-Dspring.profiles.active=docker", \
+"-Dpaxtools.model.safeset=list", \
+"-Dpaxtools.normalizer.use-latest-registry=true", \
+"-jar", "/cpath2.war", "--server"]
 EXPOSE 8080

README.md

@@ -57,6 +57,11 @@ Expect that most queries or example links won't return any result as there are n
 instance; try to find e.g. all the pathways there with `http://localhost:8080/search?q=*&type=pathway` 
 (remove `type` parameter to list all the objects; use "Accept:application/xml" header to get XML instead of JSON result).
 
+Alternatively, can run/debug the demo/dev app as:
+
+    mvn spring-boot:run
+
+
 ## Configuration
 
 ### Working directory
@@ -94,7 +99,8 @@ Copy the latest paxtools.jar into this current directory and run -
     sh export.sh 2>&1 >console.out & 
 
 (- which takes overnight or a day and night); upload/copy/move (but keep at least blacklist.txt, *All.BIOPAX.owl.gz)
-all the files from this here and ../data/ directories to the file server, or configure so that they can be downloaded from e.g. `http://www.pathwaycommons.org/archives/PC2/v{version_number}` (or else).
+all the files from this here and ../data/ directories to the file server, or configure so that they can be downloaded 
+from e.g. `http://www.pathwaycommons.org/archives/PC2/v{version_number}` (or else).
 
 Once the instance is configured and data processed, run the web service using the same 
 script as follows:
@@ -116,7 +122,7 @@ simply include to the cpath2.sh Java options like:
 ### Data
 
 One (a data manager) has to find, download, re-pack (zip) and put original 
-biological pathway data files to the data/ sub-directory.
+biological pathway data files to the data/ subdirectory.
 
 #### Warehouse data
 
@@ -138,3 +144,21 @@ Prepare original BioPAX and PSI-MI/PSI-MITAB data archives in the 'data' folder
  - download (wget) original files or archives from the pathway resource (e.g., `wget http://www.reactome.org/download/current/biopax3.zip`) 
  - extract what you need (e.g. some species data only)
  - create a new zip archive using name like `<IDENTIFIER>.zip` (datasource identifier, e.g., `reactome_human.zip`).
+
+
+## Docker
+
+### build the project and image from sources
+```
+mvn clean install
+mvn dockerfile:build
+#mvn dockerfile:tag
+#mvn dockerfile:push
+```
+
+### run
+Run with docker (can also do with compose or terraform).
+Have to bind /work dir (test/demo instance data is in the target/work)
+```
+docker run --rm --name cpath2 -v '<fullpath_to>/target/work:/work' -p 8080:8080 -it pathwaycommons/cpath2
+```