Set version to 1.0.2.

JULIELab · Jan 2, 2024 · 0530757 · 0530757
1 parent 1604934
commit 0530757
Show file tree

Hide file tree

Showing 18 changed files with 34 additions and 29 deletions.
diff --git a/gepi/README.md b/gepi/README.md
@@ -4,6 +4,12 @@
 
 The core of GePI is a web application for the user-friendly retrieval of descriptions of biomolecular interactions from the scientific literature, [PubMed](https://pubmed.ncbi.nlm.nih.gov/) (PM) and the [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/) (PMC) [open access subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/). To this end, [JCoRe](https://github.com/JULIELab/jcore-base) pipeline components are used to form a number of [UIMA](https://uima.apache.org/) pipelines for the processing of PM and PMC in order to extract the interactions.
 
+## Reference for this work
+
+GePI is described in
+
+Erik Faessler, Udo Hahn, Sascha Schäuble, GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions, *Nucleic Acids Research*, Volume 51, Issue W1, 5 July 2023, Pages W237–W242, https://doi.org/10.1093/nar/gkad445
+
 ## Overview of databases and processes to create a GePI instance from scratch
 
 A complete, running GePI web application requires the following databases, resources, pipelines and tools to be available.
@@ -18,9 +24,8 @@ Resources:
 * PubMed and PMC XML files.
 
 [UIMA pipelines](#automatic-extraction-of-interactions-from-the-literature):
-* interaction extraction NLP pipeline (does not require gene concept data from the Neo4j database),
-* indexing pipeline that sends extracted information in
-to ElasticSearch for indexing (requires gene concept data from the Neo4j database and can thus be only run successfully after the concept database has been built).
+* interaction extraction NLP pipeline,
+* extraction indexing pipeline for indexing into ElasticSearch.
 
 Tools:
 * the CoStoSys executable JAR to import PubMed/PMC XML files into the PostgreSQL database,
@@ -67,8 +72,8 @@ The `production` stage expects that the complete GePI project has been built in
 Run the following commands to create a `development` container:
 
 ```bash
-DOCKER_BUILDKIT=1 docker build -t gepi-dev:1.0.1 --target development .
-docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION=<path to config file> --name gepi-dev gepi-dev:1.0.1
+DOCKER_BUILDKIT=1 docker build -t gepi-dev:1.0.2 --target development .
+docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION=<path to config file> --name gepi-dev gepi-dev:1.0.2
 ```
 
 The first command builds an image of the `development` stage. This will also build the `dependencies` stage where all the Java dependencies of the GePI application are downloaded and cached. This will take a while on the first execution but should be faster afterwards thanks to caching.
@@ -86,8 +91,8 @@ To run the `production` container, run
 
 ```bash
 mvn clean package --projects gepi-webapp --also-make
-DOCKER_BUILDKIT=1 docker build -t gepi:1.0.1 --target production .
-docker run -dp 8080:8080 --name gepi gepi:1.0.1
+DOCKER_BUILDKIT=1 docker build -t gepi:1.0.2 --target production .
+docker run -dp 8080:8080 --name gepi gepi:1.0.2
 ```
 
 These commands
@@ -116,7 +121,7 @@ gepi.neo4j.bolt.url=bolt://<host>:<port>
 
 A production environment has a few requirements that are of lesser importance during development. This section explains requirements and solutions that may come up during GePI deployment with the Docker container. While detailed explanations come below, the full Docker `run` command we use for deployment looks like the following:
 ```
-docker run -dp 80:8080 -p 443:8443 -v /host/path/to/certificate.p12:/var/lib/jetty/etc/keystore.p12 -v /host/path/to/configuration.properties:/gepi-webapp-configuration.properties --add-host=host.docker.internal:host-gateway --name gepi -e GEPI_CONFIGURATION=/gepi-webapp-configuration.properties gepi:1.0.1 jetty.sslContext.keyStorePassword=<changeit>
+docker run -dp 80:8080 -p 443:8443 -v /host/path/to/certificate.p12:/var/lib/jetty/etc/keystore.p12 -v /host/path/to/configuration.properties:/gepi-webapp-configuration.properties --add-host=host.docker.internal:host-gateway --name gepi -e GEPI_CONFIGURATION=/gepi-webapp-configuration.properties gepi:1.0.2 jetty.sslContext.keyStorePassword=<changeit>
 ```
 Alternatively, the `docker-compose-webapp.yml` file can be used with a few additions.
 

diff --git a/gepi/docker-compose-webapp.yml b/gepi/docker-compose-webapp.yml
@@ -1,7 +1,7 @@
 version: "3.2"
 services:
   gepi:
-    image: gepi:1.0.1
+    image: gepi:1.0.2
     container_name: gepi
     ports:
       - 0.0.0.0:80:8080

diff --git a/gepi/docker-compose-with-es.yml b/gepi/docker-compose-with-es.yml
@@ -1,6 +1,6 @@
 services:
   gepi:
-    image: gepi:1.0.1
+    image: gepi:1.0.2
     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>1.0.1</version>
+		<version>1.0.2</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 	<artifactId>gepi-concept-database</artifactId>

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>1.0.1</version>
+        <version>1.0.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <dependencies>

diff --git a/gepi/gepi-indexing/gepi-indexing-base/component.meta b/gepi/gepi-indexing/gepi-indexing-base/component.meta
@@ -18,7 +18,7 @@
     "maven-artifact": {
         "artifactId": "gepi-indexing-base",
         "groupId": "de.julielab",
-        "version": "1.0.1"
+        "version": "1.0.2"
     },
     "name": "GePi Indexing Base"
 }
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>1.0.1</version>
+        <version>1.0.2</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>1.0.1</version>
+        <version>1.0.2</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>1.0.1</version>
+            <version>1.0.2</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>1.0.1</version>
+        <version>1.0.2</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>1.0.1</version>
+            <version>1.0.2</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>1.0.1</version>
+    <version>1.0.2</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>1.0.1</version>
+      <version>1.0.2</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>1.0.1</version>
+    <version>1.0.2</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>1.0.1</version>
+      <version>1.0.2</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>1.0.1</version>
+        <version>1.0.2</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>1.0.1</version>
+        <version>1.0.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
     <modelVersion>4.0.0</modelVersion>

diff --git a/gepi/gepi-webapp/pom.xml b/gepi/gepi-webapp/pom.xml
@@ -224,7 +224,7 @@ of testing facilities designed for use with TestNG (http://testng.org/), so it's
     <parent>
         <groupId>de.julielab</groupId>
         <artifactId>gepi</artifactId>
-        <version>1.0.1</version>
+        <version>1.0.2</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 </project>
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
@@ -64,7 +64,7 @@ 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, "1.0.1");
+        configuration.override(SymbolConstants.APPLICATION_VERSION, "1.0.2");
         // Avoid Ajax-requests waiting for each other. This would make asynchronous lading of
         // dashboard elements impossible
         configuration.override(SymbolConstants.SESSION_LOCKING_ENABLED, false);

diff --git a/gepi/gepi-webapp/src/main/resources/de/julielab/gepi/webapp/components/Layout.tml b/gepi/gepi-webapp/src/main/resources/de/julielab/gepi/webapp/components/Layout.tml
@@ -39,7 +39,7 @@
                             <t:EventLink id="resetlink" event="reset" class="nav-link">Reset Session</t:EventLink>
                         </li>
                     </ul>
-                   <!-- <span class="ms-5 navbar-text">application version ${symbol:tapestry.application-version}</span>-->
+                    <span class="ms-5 navbar-text">GePI Version ${symbol:tapestry.application-version}</span>
 <!--                    <ul id="filteroptions" class="nav navbar-nav hidden">-->
 <!--                        <li class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" aria-expanded="false">Results Filter <span class="caret"/></a>-->
 <!--                            <ul class="dropdown-menu">-->

diff --git a/gepi/pom.xml b/gepi/pom.xml
@@ -7,7 +7,7 @@
         <version>2.5.0</version>
     </parent>
     <artifactId>gepi</artifactId>
-    <version>1.0.1</version>
+    <version>1.0.2</version>
     <name>GePi</name>
     <description>The GePi parent project.</description>
     <packaging>pom</packaging>

diff --git a/gepi/readme-raw/README.md b/gepi/readme-raw/README.md
@@ -159,5 +159,5 @@ Update the new version number in the following places:
   * set `PRODUCTION_MODE` to true for releases
 * the Docker image version in the `docker-compose.yml`
 * the DB version in `gene-database.xml` in the `gepi-concept-database` module
-* 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
+* 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 base directory as GePI
   * this updates the description file for the use with the JCoRe pipeline builder