Merge branch 'master' of https://github.com/JULIELab/gepi

JULIELab · Jul 13, 2022 · 42d2242 · 42d2242
2 parents 3fd5667 + 415a182
commit 42d2242
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Showing 17 changed files with 27 additions and 24 deletions.
diff --git a/gepi/docker-compose.yml b/gepi/docker-compose.yml
@@ -1,6 +1,6 @@
 services:
   gepi:
-    image: gepi:0.2.0-SNAPSHOT
+    image: gepi:0.8.0-SNAPSHOT
     container_name: gepi
     ports:
       - 0.0.0.0:80:8080

diff --git a/gepi/gepi-concept-database/pom.xml b/gepi/gepi-concept-database/pom.xml
@@ -4,7 +4,7 @@
 	<parent>
 		<groupId>de.julielab</groupId>
 		<artifactId>gepi</artifactId>
-		<version>0.2.0-SNAPSHOT</version>
+		<version>0.8.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>gepi-concept-database</artifactId>
 	<name>GePi Concept Database</name>

diff --git a/gepi/gepi-core/pom.xml b/gepi/gepi-core/pom.xml
@@ -7,7 +7,7 @@
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>gepi</artifactId>
-        <version>0.2.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <dependencies>

diff --git a/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/GePiDataService.java b/gepi/gepi-core/src/main/java/de/julielab/gepi/core/services/GePiDataService.java
@@ -248,7 +248,7 @@ public File getOverviewExcel(List<Event> events, long dataSessionId, EnumSet<Inp
     }
 
     private void createExcelSummaryFile(File tsvFile, File xlsFile, EnumSet<InputMode> inputMode, String sentenceFilterString, String paragraphFilterString, String sectionNameFilterString) throws IOException {
-        ProcessBuilder builder = new ProcessBuilder().command("python", "-c", excelResultCreationScript, tsvFile.getAbsolutePath(), xlsFile.getAbsolutePath(), inputMode.stream().map(InputMode::name).collect(Collectors.joining(" ")), sentenceFilterString != null ? sentenceFilterString : "<none>", paragraphFilterString != null ? paragraphFilterString : "<none>", sectionNameFilterString != null ? sectionNameFilterString : "<none>");
+        ProcessBuilder builder = new ProcessBuilder().command("python3", "-c", excelResultCreationScript, tsvFile.getAbsolutePath(), xlsFile.getAbsolutePath(), inputMode.stream().map(InputMode::name).collect(Collectors.joining(" ")), sentenceFilterString != null ? sentenceFilterString : "<none>", paragraphFilterString != null ? paragraphFilterString : "<none>", sectionNameFilterString != null ? sectionNameFilterString : "<none>");
         Process process = builder.start();
         InputStream processInput = process.getInputStream();
         InputStream processErrors = process.getErrorStream();

diff --git a/gepi/gepi-indexing/gepi-indexing-base/pom.xml b/gepi/gepi-indexing/gepi-indexing-base/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi-indexing</artifactId>
         <groupId>de.julielab</groupId>
-        <version>0.8.1-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/gepi/gepi-indexing/gepi-indexing-debug/pom.xml b/gepi/gepi-indexing/gepi-indexing-debug/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi-indexing</artifactId>
         <groupId>de.julielab</groupId>
-        <version>0.8.1-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>gepi-indexing-base</artifactId>
-            <version>0.8.1-SNAPSHOT</version>
+            <version>0.8.0-SNAPSHOT</version>
         </dependency>
     </dependencies>
 </project>
diff --git a/gepi/gepi-indexing/gepi-indexing-pmc/pom.xml b/gepi/gepi-indexing/gepi-indexing-pmc/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi-indexing</artifactId>
         <groupId>de.julielab</groupId>
-        <version>0.8.1-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
         <dependency>
             <groupId>de.julielab</groupId>
             <artifactId>gepi-indexing-base</artifactId>
-            <version>0.8.1-SNAPSHOT</version>
+            <version>0.8.0-SNAPSHOT</version>
         </dependency>
     </dependencies>
 </project>
diff --git a/gepi/gepi-indexing/gepi-indexing-pubmed/pom.xml b/gepi/gepi-indexing/gepi-indexing-pubmed/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>gepi-indexing</artifactId>
     <groupId>de.julielab</groupId>
-    <version>0.8.1-SNAPSHOT</version>
+    <version>0.8.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
   <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
     <dependency>
       <groupId>de.julielab</groupId>
       <artifactId>gepi-indexing-base</artifactId>
-      <version>0.8.1-SNAPSHOT</version>
+      <version>0.8.0-SNAPSHOT</version>
     </dependency>
   </dependencies>
 </project>
diff --git a/gepi/gepi-indexing/gepi-indexing-testdata/pom.xml b/gepi/gepi-indexing/gepi-indexing-testdata/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <artifactId>gepi-indexing</artifactId>
     <groupId>de.julielab</groupId>
-    <version>0.8.1-SNAPSHOT</version>
+    <version>0.8.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
   <modelVersion>4.0.0</modelVersion>
@@ -15,7 +15,7 @@
     <dependency>
       <groupId>de.julielab</groupId>
       <artifactId>gepi-indexing-base</artifactId>
-      <version>0.8.1-SNAPSHOT</version>
+      <version>0.8.0-SNAPSHOT</version>
     </dependency>
   </dependencies>
 </project>
diff --git a/gepi/gepi-indexing/pom.xml b/gepi/gepi-indexing/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi</artifactId>
         <groupId>de.julielab</groupId>
-        <version>0.8.1-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <packaging>pom</packaging>

diff --git a/gepi/gepi-test-data/pom.xml b/gepi/gepi-test-data/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>gepi</artifactId>
         <groupId>de.julielab</groupId>
-        <version>0.2.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/gepi/gepi-webapp/Dockerfile b/gepi/gepi-webapp/Dockerfile
@@ -1,5 +1,8 @@
 # syntax=docker/dockerfile:1
 
 FROM jetty:10.0.9-jre11-slim-openjdk
+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-to-startd=https
 COPY target/gepi-webapp.war /var/lib/jetty/webapps/ROOT.war
diff --git a/gepi/gepi-webapp/README.md b/gepi/gepi-webapp/README.md
@@ -20,13 +20,13 @@ The easiest way to get a running GePi webapp is the usage of Docker. For this pu
 To build the WAR, use the Maven build tool. From within the `gepi-webapp` folder, use `mvn clean package -f ../pom.xml --projects gepi-webapp --also-make`
 <div style="border: 4px solid #77C0CA; margin-left:50px; border-radius: 20px; width: 400px;padding: 10px">Of course you can also build the project in the GePi root directory. Then you just need to omit the <textit style="background-color:#F3F6F8">-f ../pom.xml</textit> portion.</div>
 
-After a successful Maven build, navigate to the `gepi-webapp` directory and execute the following command: `docker build -t gepi:0.2.0-SNAPSHOT .`
+After a successful Maven build, navigate to the `gepi-webapp` directory and execute the following command: `docker build -t gepi:0.8.0-SNAPSHOT .`
 
-To create an app container, type `docker run -dp 8080:8080 gepi:0.2.0-SNAPSHOT`. Navigate to `localhost:8080` in your browser and you should see the landing page of GePi.
+To create an app container, type `docker run -dp 8080:8080 gepi:0.8.0-SNAPSHOT`. Navigate to `localhost:8080` in your browser and you should see the landing page of GePi.
 
 Note however, the searching will only work if the Neo4j and ElasticSearch services are available at the locations specified in `src/main/resources/configuration.properties.jetty`.
 
 ## Required Python Packages for Result Excel Sheet Creation
 
-* openpyxl
-* xlsxwriter
+* openpyxl v3.0.9
+* xlsxwriter v3.0.1
diff --git a/gepi/gepi-webapp/pom.xml b/gepi/gepi-webapp/pom.xml
@@ -238,7 +238,7 @@ of testing facilities designed for use with TestNG (http://testng.org/), so it's
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>gepi</artifactId>
-        <version>0.2.0-SNAPSHOT</version>
+        <version>0.8.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 </project>
diff --git a/gepi/gepi-webapp/readme-raw/README.md b/gepi/gepi-webapp/readme-raw/README.md
@@ -28,5 +28,5 @@ Note however, the searching will only work if the Neo4j and ElasticSearch servic
 
 ## Required Python Packages for Result Excel Sheet Creation
 
-* openpyxl
-* xlsxwriter
+* openpyxl v3.0.9
+* xlsxwriter v3.0.1
diff --git a/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/services/AppModule.java b/gepi/gepi-webapp/src/main/java/de/julielab/gepi/webapp/services/AppModule.java
@@ -53,7 +53,7 @@ public static void contributeFactoryDefaults(
 
         // The application version is primarily useful as it appears in
         // any exception reports (HTML or textual).
-        configuration.override(SymbolConstants.APPLICATION_VERSION, "0.8.1-beta");
+        configuration.override(SymbolConstants.APPLICATION_VERSION, "0.8.0-beta2");
 
         // This is something that should be removed when going to production, but is useful
         // in the early stages of development.

diff --git a/gepi/pom.xml b/gepi/pom.xml
@@ -7,7 +7,7 @@
         <version>2.4.1</version>
     </parent>
     <artifactId>gepi</artifactId>
-    <version>0.8.1-SNAPSHOT</version>
+    <version>0.8.0-SNAPSHOT</version>
     <name>GePi</name>
     <description>The GePi parent project.</description>
     <packaging>pom</packaging>