Merge pull request #221 from JULIELab/download_link

Fix #220.

gepi/Dockerfile

@@ -39,5 +39,5 @@ FROM jetty:10.0.9-jre11-slim-openjdk as production
 USER root
 RUN apt-get update -y && apt-get install -y python3.9 && apt-get install -y python3-pip && pip install pandas==1.3.2 openpyxl==3.0.9 xlsxwriter==3.0.1
 USER jetty
-RUN java -jar "$JETTY_HOME/start.jar" --add-modules=ssl,https
+#RUN java -jar "$JETTY_HOME/start.jar" --add-modules=ssl,https
 COPY gepi-webapp/target/gepi-webapp.war /var/lib/jetty/webapps/ROOT.war

gepi/README.md

@@ -104,7 +104,7 @@ Update the new version number in the following places:
 * `README.md` (by executing `mvn clean package -DskipTests=true` to filter the `readme-raw/README.md` file to automatically set the current version to the `README.md` file)
 * `AppModule.java` in `gepi-webapp`
   * set `PRODUCTION_MODE` to true for releases
-* the Docker image version in the `docker-compose-*.yml`
+* the Docker image version in the `docker-compose.yml`
 * the DB version in `gene-database.xml` in the `gepi-concept-database` module
-* in `gepi-indexing-base` execute `python ../../../../jcore-misc/jcore-scripts/createMetaDescriptors.py -c -i -r manual -v 1.0 .` given that `jcore-misc` has been cloned to the same directory as GePI
+* in execute `python ../../jcore-misc/jcore-scripts/createMetaDescriptors.py -c -i -r manual -v 1.0 gepi-indexing/gepi-indexing-base` given that `jcore-misc` has been cloned to the same directory as GePI
   * this updates the description file for the use with the JCoRe pipeline builder

gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/GePiDataService.java

@@ -33,10 +33,22 @@ public class GePiDataService implements IGePiDataService {
     public static final String GEPI_TMP_DIR_NAME = "gepi";
     public static final String GEPI_EXCEL_FILE_PREFIX_NAME = "gepi-excel-";
     public static final String GEPI_EXCEL_STATUS_FILE_PREFIX = "gepi-excel-status-";
-    private static final Logger log = LoggerFactory.getLogger(GePiDataService.class);
     public static final String EXCEL_FILE_SUCCESS_STATE = "GePI interactions have been successfully saved in Excel format.";
-    private Cache<Long, GePiData> dataCache;
+    protected static final HashMap<Integer, String> likelihoodNames;
+    private static final Logger log = LoggerFactory.getLogger(GePiDataService.class);
+
+    static {
+        likelihoodNames = new HashMap<>();
+        likelihoodNames.put(1, "negation");
+        likelihoodNames.put(2, "low");
+        likelihoodNames.put(3, "investigation");
+        likelihoodNames.put(4, "moderate");
+        likelihoodNames.put(5, "high");
+        likelihoodNames.put(6, "assertion");
+    }
+
     private final Path gepiTmpDir;
+    private Cache<Long, GePiData> dataCache;
     private String excelFilePrefix;
     /**
      * This string is the scripts itself, not a reference to a file.
@@ -254,15 +266,21 @@ public JSONArray convertToJson(List<Event> eventList) {
     public Path getOverviewExcel(Future<EventRetrievalResult> eventRetrievalResult, long dataSessionId, EnumSet<InputMode> inputMode, String sentenceFilterString, String paragraphFilterString, String sectionNameFilterString) throws IOException, ExecutionException, InterruptedException {
         long time = System.currentTimeMillis();
         log.info("Creating event statistics Excel file for dataSessionId {}", dataSessionId);
-        updateDownloadFileCreationsStatus( "Step 1 of 3: Retrieving and storing all interactions for Excel sheet creation.", dataSessionId);
+        final Path tempStatusFile = getTempStatusFile(dataSessionId);
+        if (!Files.exists(tempStatusFile)) {
+            if (!Files.exists(tempStatusFile.getParent()))
+                Files.createDirectories(tempStatusFile.getParent());
+            Files.createFile(tempStatusFile);
+        }
+        updateDownloadFileCreationsStatus("Step 1 of 3: Retrieving and storing all interactions for Excel sheet creation.", dataSessionId);
         Path tsvFile = getTempTsvDataFile(dataSessionId);
         Path xlsFile = getTempXlsDataFile(dataSessionId);
         writeOverviewTsvFile(eventRetrievalResult.get().getEventList(), tsvFile);
-        updateDownloadFileCreationsStatus( "Step 2 of 3: Retrieval of all interactions has finished. Creating Excel file.", dataSessionId);
+        updateDownloadFileCreationsStatus("Step 2 of 3: Retrieval of all interactions has finished. Creating Excel file.", dataSessionId);
         createExcelSummaryFile(tsvFile, xlsFile, inputMode, sentenceFilterString, paragraphFilterString, sectionNameFilterString);
         updateDownloadFileCreationsStatus(EXCEL_FILE_SUCCESS_STATE + " The file is ready for download.", dataSessionId);
         time = System.currentTimeMillis() - time;
-        log.info("Excel sheet creation took {} seconds", time/1000);
+        log.info("Excel sheet creation took {} seconds", time / 1000);
         return xlsFile;
     }
 
@@ -305,17 +323,7 @@ private void createExcelSummaryFile(Path tsvFile, Path xlsFile, EnumSet<InputMod
         if (!Files.exists(xlsFile))
             throw new FileNotFoundException("The Excel file " + xlsFile.toAbsolutePath() + " does not exist.");
     }
-    protected static final HashMap<Integer, String> likelihoodNames;
 
-    static {
-        likelihoodNames = new HashMap<>();
-        likelihoodNames.put(1, "negation");
-        likelihoodNames.put(2, "low");
-        likelihoodNames.put(3, "investigation");
-        likelihoodNames.put(4, "moderate");
-        likelihoodNames.put(5, "high");
-        likelihoodNames.put(6, "assertion");
-    }
     private void writeOverviewTsvFile(List<Event> events, Path file) throws IOException {
         log.debug("Writing event statistics tsv file to {}", file);
         try (BufferedWriter bw = new BufferedWriter(new FileWriter(file.toFile(), UTF_8))) {

gepi/gepi-webapp/src/main/resources/logback.xml

@@ -22,12 +22,12 @@
 	<logger name="de.julielab.elastic.query.components.data.ElasticServerResponse" level="INFO"/>
 	<logger name="de.julielab" level="INFO" />
 <!--	<logger name="de.julielab.gepi.webapp" level="DEBUG"/>-->
-	<logger name="de.julielab.gepi.webapp.pages.Index" level="debug"/>
+<!--	<logger name="de.julielab.gepi.webapp.pages.Index" level="debug"/>-->
 	<logger name="de.julielab.gepi.webapp.components.GepiWidgetLayout" level="INFO"/>
 <!--	<logger name="de.julielab.gepi.core.services.GepiCoreModule.IGeneIdService" level="DEBUG"/>-->
 		<logger name="de.julielab.gepi.core.services.GepiCoreModule.IGePiDataService" level="DEBUG"/>
 <!--	<logger name="de.julielab.gepi.core.services.GepiCoreModule.IEventRetrievalService" level="DEBUG"/>-->
-	<logger	name="de.julielab.elastic.query.services.ElasticQueryComponentsModule.ElasticSearchComponent" level="TRACE" />
+<!--	<logger	name="de.julielab.elastic.query.services.ElasticQueryComponentsModule.ElasticSearchComponent" level="TRACE" />-->
 	<!--
 	<logger name="de.julielab.gepi.webapp.pages.Index" level="DEBUG"/>
 	<logger name="de.julielab.gepi.webapp.components.GepiInput" level="DEBUG"/>