1741 : solr auto exec complete

# Conflicts:
#	shanoir-ng-datasets/src/main/java/org/shanoir/ng/solr/service/SolrServiceImpl.java

# Conflicts:
#	shanoir-ng-datasets/src/main/java/org/shanoir/ng/solr/service/SolrServiceImpl.java

docker-compose-dev.yml

@@ -213,6 +213,7 @@ services:
       - "database"
       - "rabbitmq"
       - "users"
+      - "solr"
 
   preclinical:
     container_name: "${SHANOIR_PREFIX}preclinical"

docker-compose/Dockerfile

@@ -80,7 +80,6 @@ RUN wget -qO dcm4che-bin.zip \
     && unzip /dcm4che-bin.zip && mv dcm4che-* dcm4che \
     && rm    /dcm4che-bin.zip
 
-
 FROM base-microservice as datasets
 
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
@@ -91,6 +90,9 @@ RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     locales \
     locales-all
 
+RUN apt-get install -y iputils-ping
+
+
 # take care of path
 ENV PATH /opt/dcm4che/bin:$PATH
 ENV LC_ALL en_US.UTF-8
@@ -99,16 +101,21 @@ ENV LANGUAGE en_US.UTF-8
 
 # install the files from the 'dowloader' stage
 COPY --link --from=datasets-download /target/. /
+COPY --link datasets/shanoir-ng-datasets.jar shanoir-ng-datasets.jar
+
+
 
 COPY --link datasets/entrypoint /usr/bin/
-COPY --link datasets/shanoir-ng-datasets.jar shanoir-ng-datasets.jar
+COPY --link datasets/wait-for-solr.sh /usr/bin/
 
-# Use the below line for remote debugging
+ # Use the below line for remote debugging
 #CMD ["-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=0.0.0.0:9914", "-jar", "/shanoir-ng-datasets.jar"]
 CMD ["-jar", "/shanoir-ng-datasets.jar"]
 
 
 
+
+
 ################ import ####################################################
 
 FROM base-microservice as import
@@ -387,6 +394,8 @@ RUN mkdir -p /etc/shanoir-core-template \
 USER solr
 
 COPY --link solr/core /etc/shanoir-core-template/
+COPY --link solr/entrypoint /usr/bin/
 
+ENTRYPOINT ["/usr/bin/entrypoint"]
 CMD ["solr-precreate", "shanoir", "/etc/shanoir-core-template"]
 

docker-compose/datasets/entrypoint

@@ -19,4 +19,6 @@ handle_microservice_migration
 
 abort_if_error
 
-run_microservice "$@"
+/usr/bin/wait-for-solr.sh
+
+run_microservice "$@"

docker-compose/datasets/wait-for-solr.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+WAIT_TIME=300
+
+echo "Waiting for the solr container to be reachable..."
+
+# Try pinging the solr container
+while ! ping -c 1 -W 1 "solr" > /dev/null 2>&1; do
+  echo "Container solr is not reachable, retrying..."
+  sleep 5
+
+  # Decrement wait time and exit if it reaches zero
+  WAIT_TIME=$((WAIT_TIME - 1))
+  if [ "$WAIT_TIME" -le 0 ]; then
+    echo "Error : Timeout waiting for container solr to become reachable."
+    exit 1
+  fi
+done
+
+echo "Container solr reached, launching container datasets."

docker-compose/solr/entrypoint

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -e
+(
+  # Compare old and new solr scheme.xml
+  set -e
+  cd /etc/shanoir-core-template
+  for file in $(find . -maxdepth 1 -type f); do
+    cmp -- "$file" "/var/solr/data/shanoir/$file"
+  done
+  echo "Solr index is up-to-date, no rebuild needed"
+) || (
+  # If different, remove last index
+  echo 'Deleting /var/solr/data (not up-to-date with the template), the index has to be rebuilt'
+  rm -rf /var/solr/data
+)
+
+$@

shanoir-ng-datasets/src/main/java/org/shanoir/ng/ShanoirDatasetIndexation.java

@@ -0,0 +1,41 @@
+package org.shanoir.ng;
+
+import org.apache.solr.client.solrj.SolrClient;
+import org.apache.solr.client.solrj.SolrQuery;
+import org.shanoir.ng.solr.service.SolrServiceImpl;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.ApplicationArguments;
+import org.springframework.boot.ApplicationRunner;
+import org.springframework.context.annotation.Profile;
+import org.springframework.stereotype.Component;
+
+import java.util.Objects;
+
+
+@Component
+@Profile("!test")
+public class ShanoirDatasetIndexation implements ApplicationRunner {
+
+    @Autowired
+    private SolrClient solrClient;
+
+    @Autowired
+    private SolrServiceImpl solrServiceImpl;
+
+    private static final Logger LOG = LoggerFactory.getLogger(ShanoirDatasetIndexation.class);
+
+    @Override
+    public void run(ApplicationArguments args) throws Exception {
+        SolrQuery q = new SolrQuery("*:*");
+        q.setRows(0);  // don't actually request any data
+        if(Objects.nonNull(solrClient.query(q)) && Objects.equals(0L, solrClient.query(q).getResults().getNumFound())){
+            LOG.info("Solr index empty. Re-indexing...");
+            solrServiceImpl.indexAllNoAuth();
+            LOG.info("Solr indexation complete.");
+        } else {
+            LOG.info("Solr index already complete, no re-indexation required.");
+        }
+    }
+}

shanoir-ng-datasets/src/main/java/org/shanoir/ng/solr/service/SolrServiceImpl.java

@@ -56,7 +56,6 @@
 import org.springframework.data.domain.Sort;
 import org.springframework.data.solr.core.query.result.SolrResultPage;
 import org.springframework.scheduling.annotation.Async;
-import org.springframework.scheduling.annotation.Scheduled;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Isolation;
 import org.springframework.transaction.annotation.Propagation;
@@ -195,6 +194,29 @@ protected ShanoirEvent beginIndexationProcess() {
 		return event;
 	}
 
+    @Async
+    @Transactional
+    public void indexAllNoAuth() {
+        List<ShanoirMetadata> documents = new ArrayList<>();
+        Map<Long, List<String>> tags = new HashMap<>();
+        ShanoirEvent event;
+
+        try {
+            event = new ShanoirEvent(
+                    ShanoirEventType.SOLR_INDEX_ALL_EVENT,
+                    null,
+                    0L,
+                    "Cleaning Solr index...",
+                    ShanoirEvent.IN_PROGRESS,
+                    0f);
+            eventService.publishEvent(event);
+            cleanOldIndex(event);
+            fetchDatasToIndex(event, documents, tags);
+            indexDatas(event, documents, tags);
+        } catch (SolrServerException | IOException ignored) {
+        }
+    }
+
 	@Transactional
 	@Override
 	public void indexDatasets(List<Long> datasetIds) throws SolrServerException, IOException {