Merge pull request #211 from ipb-halle/reporting

Disentangle text extraction and reporting from ui
ipb-halle · Nov 15, 2023 · 09263b7 · 09263b7
2 parents 1cafbf2 + bf5ebe3
commit 09263b7
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Showing 359 changed files with 10,563 additions and 4,148 deletions.
diff --git a/agency/pom.xml b/agency/pom.xml
@@ -76,7 +76,7 @@
         </descriptorRefs>
         <archive>
           <manifest>
-            <mainClass>de.ipb_halle.lbac.device.job.Agency</mainClass>
+            <mainClass>de.ipb_halle.job.Agency</mainClass>
           </manifest>
          </archive>
       </configuration>
@@ -133,7 +133,7 @@
 
                     <transformers>
                         <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                            <mainClass>de.ipb_halle.lbac.device.job.Agency</mainClass>
+                            <mainClass>de.ipb_halle.job.Agency</mainClass>
                         </transformer>
 
                         <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
@@ -179,10 +179,10 @@
     <version>1.3.1</version>
   </dependency>
 
-  <!-- crimsy-agency-api -->
+  <!-- crimsy-job-api -->
   <dependency>
     <groupId>de.ipb-halle</groupId>
-    <artifactId>crimsy-agency-api</artifactId>
+    <artifactId>crimsy-job-api</artifactId>
     <version>1.0</version>
   </dependency>
 

diff --git a/.../de/ipb_halle/lbac/device/job/Agency.java → ...rc/main/java/de/ipb_halle/job/Agency.java b/.../de/ipb_halle/lbac/device/job/Agency.java → ...rc/main/java/de/ipb_halle/job/Agency.java
@@ -1,6 +1,6 @@
 /*
  * CRIMSy Agency
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 import java.io.BufferedReader;
 import java.io.FileReader;

diff --git a/...de/ipb_halle/lbac/device/job/Handler.java → ...c/main/java/de/ipb_halle/job/Handler.java b/...de/ipb_halle/lbac/device/job/Handler.java → ...c/main/java/de/ipb_halle/job/Handler.java
@@ -1,6 +1,6 @@
 /*
  * CRIMSy Agency
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 import java.io.IOException;
 import java.util.List;

diff --git a/agency/util/bin/testSetup.sh b/agency/util/bin/testSetup.sh
@@ -20,7 +20,8 @@ java -Djavax.net.ssl.trustStore=./truststore \\
   -jar ../target/crimsy-agency-1.0.jar \\
   -p ./agency_secret.txt \\
   -s ./agent.sh \\
-  -u https://biocloud.somewhere.invalid/ui/rest/jobs
+  -t PRINT \\
+  -u https://biocloud.somewhere.invalid/ui/rest/print
 EOF
 
 cat <<EOF > test/agent.sh
@@ -40,9 +41,10 @@ cat <<EOF
 
 Please note: 
 1. This setup is not for production runs.
-2. You still need to tweak the configuration:
+2. You still need to tweak lots of configuration:
    - copy truststore and truststore password files
    - shared secret of your CRIMSy node
    - URL of your CRIMSY node
+   - meaningful job script (e.g. to submit print jobs), logging, ...
 
 EOF
diff --git a/agency-api/pom.xml → crimsy-api/pom.xml b/agency-api/pom.xml → crimsy-api/pom.xml
@@ -1,7 +1,7 @@
 <!--
  
   Leibniz Bioactives Cloud
-  Copyright 2017 Leibniz-Institut f. Pflanzenbiochemie
+  Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  
   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
@@ -23,11 +23,11 @@
  <modelVersion>4.0.0</modelVersion>
 
  <groupId>de.ipb-halle</groupId>
- <artifactId>crimsy-agency-api</artifactId>
- <version>1.0</version>
+ <artifactId>crimsy-api</artifactId>
+ <version>1.0.0</version>
  <packaging>jar</packaging>
 
- <name>CRIMSy Agency API</name>
+ <name>CRIMSy-API</name>
  <url>http://github.com/ipb-halle/CRIMSy</url>
 
  <properties>

diff --git a/..._halle/lbac/search/lang/AttributeTag.java → ...de/ipb_halle/crimsy_api/AttributeTag.java b/..._halle/lbac/search/lang/AttributeTag.java → ...de/ipb_halle/crimsy_api/AttributeTag.java
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.search.lang;
+package de.ipb_halle.crimsy_api;
 
 import java.lang.annotation.Documented;
 import java.lang.annotation.ElementType;

diff --git a/...halle/lbac/search/lang/AttributeType.java → ...e/ipb_halle/crimsy_api/AttributeType.java b/...halle/lbac/search/lang/AttributeType.java → ...e/ipb_halle/crimsy_api/AttributeType.java
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.search.lang;
+package de.ipb_halle.crimsy_api;
 
 /**
  * Attribute types for selection of search fields

diff --git a/...in/java/de/ipb_halle/lbac/entity/DTO.java → ...ain/java/de/ipb_halle/crimsy_api/DTO.java b/...in/java/de/ipb_halle/lbac/entity/DTO.java → ...ain/java/de/ipb_halle/crimsy_api/DTO.java
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.entity;
+package de.ipb_halle.crimsy_api;
 
 public interface DTO<T> {
 

diff --git a/agency-api/LICENSE → crimsy-job-api/LICENSE b/agency-api/LICENSE → crimsy-job-api/LICENSE
diff --git a/agency-api/README.md → crimsy-job-api/README.md b/agency-api/README.md → crimsy-job-api/README.md
@@ -1,4 +1,4 @@
-# crimsy-agency-api
+# crimsy-job-api
 
 API for communication between CRIMSy and crimsy-agency.
 

diff --git a/crimsy-job-api/pom.xml b/crimsy-job-api/pom.xml
@@ -0,0 +1,129 @@
+<!--
+ 
+  Leibniz Bioactives Cloud
+  Copyright 2017 Leibniz-Institut f. Pflanzenbiochemie
+ 
+  Licensed under the Apache License, Version 2.0 (the "License");
+  you may not use this file except in compliance with the License.
+  You may obtain a copy of the License at
+ 
+      http://www.apache.org/licenses/LICENSE-2.0
+ 
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+ 
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
+ http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>de.ipb-halle</groupId>
+ <artifactId>crimsy-job-api</artifactId>
+ <version>1.0</version>
+ <packaging>jar</packaging>
+
+ <name>CRIMSy Job API</name>
+ <url>http://github.com/ipb-halle/CRIMSy</url>
+
+ <properties>
+  <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+
+  <!-- check Maven Central for latest versions! -->
+ </properties>
+
+ <!-- define (additional) repositories -->
+ <repositories>
+    <repository>
+      <id>central</id>
+      <url>https://repo.maven.apache.org/maven2/</url>
+   </repository>
+   <repository>
+     <id>sonatype public</id>
+     <url>https://oss.sonatype.org/content/groups/public/</url>
+   </repository>
+ </repositories>
+
+
+ <build>
+  <plugins>
+
+   <!-- compile plugin -->
+   <plugin>
+    <groupId>org.apache.maven.plugins</groupId>
+    <artifactId>maven-compiler-plugin</artifactId>
+    <version>3.1</version>
+    <configuration>
+     <source>1.8</source>
+     <target>1.8</target>
+     <compilerArgument>-Xlint:all</compilerArgument>
+     <encoding>${project.build.sourceEncoding}</encoding>
+    </configuration>
+   </plugin>
+
+    <!-- assembly plugin -->
+    <plugin>
+      <artifactId>maven-assembly-plugin</artifactId>
+      <version>2.6</version>
+      <configuration>
+        <descriptorRefs>
+          <descriptorRef>jar-with-dependencies</descriptorRef> 
+        </descriptorRefs>
+        <archive>
+          <manifest>
+          </manifest>
+         </archive>
+      </configuration>
+
+      <executions>
+          <execution>
+            <id>make-assembly</id>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+          </execution>
+      </executions>
+    </plugin>
+
+  </plugins>
+ </build>
+
+  <dependencies>
+
+        <!-- CRIMSy API -->
+        <dependency>
+            <groupId>de.ipb-halle</groupId>
+            <artifactId>crimsy-api</artifactId>
+            <version>1.0.0</version>
+        </dependency>
+
+        <!-- tomee JAX-RS -->
+        <dependency>
+            <groupId>org.apache.tomee</groupId>
+            <artifactId>tomee-jaxrs</artifactId>
+            <version>7.0.5</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <!-- unit testing -->
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.13.1</version>
+            <scope>test</scope>
+        </dependency>
+
+        <!-- SLF4J -->
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+            <version>1.7.30</version>
+        </dependency>
+
+  </dependencies>
+</project>
diff --git a/.../ipb_halle/lbac/device/job/JobStatus.java → ...main/java/de/ipb_halle/job/JobStatus.java b/.../ipb_halle/lbac/device/job/JobStatus.java → ...main/java/de/ipb_halle/job/JobStatus.java
@@ -1,6 +1,6 @@
 /*
  * Cloud Resource & Information Management System (CRIMSy)
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 import javax.xml.bind.annotation.XmlEnum;
 

diff --git a/...de/ipb_halle/lbac/device/job/JobType.java → ...c/main/java/de/ipb_halle/job/JobType.java b/...de/ipb_halle/lbac/device/job/JobType.java → ...c/main/java/de/ipb_halle/job/JobType.java
@@ -1,6 +1,6 @@
 /*
  * Cloud Resource & Information Management System (CRIMSy)
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 import javax.xml.bind.annotation.XmlEnum;
 

diff --git a/...b_halle/lbac/device/job/JobWebClient.java → ...n/java/de/ipb_halle/job/JobWebClient.java b/...b_halle/lbac/device/job/JobWebClient.java → ...n/java/de/ipb_halle/job/JobWebClient.java
@@ -1,6 +1,6 @@
 /*
  * Cloud Resource & Information Management System (CRIMSy)
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 
 import javax.ws.rs.core.MediaType;

diff --git a/.../de/ipb_halle/lbac/device/job/NetJob.java → ...rc/main/java/de/ipb_halle/job/NetJob.java b/.../de/ipb_halle/lbac/device/job/NetJob.java → ...rc/main/java/de/ipb_halle/job/NetJob.java
@@ -1,6 +1,6 @@
 /*
  * Cloud Resource & Information Management System (CRIMSy)
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 import java.io.Serializable;
 

diff --git a/...pb_halle/lbac/device/job/RequestType.java → ...in/java/de/ipb_halle/job/RequestType.java b/...pb_halle/lbac/device/job/RequestType.java → ...in/java/de/ipb_halle/job/RequestType.java
@@ -1,6 +1,6 @@
 /*
  * Cloud Resource & Information Management System (CRIMSy)
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 import javax.xml.bind.annotation.XmlEnum;
 

diff --git a/...halle/lbac/device/job/TokenGenerator.java → ...java/de/ipb_halle/job/TokenGenerator.java b/...halle/lbac/device/job/TokenGenerator.java → ...java/de/ipb_halle/job/TokenGenerator.java
@@ -1,6 +1,6 @@
 /*
  * Cloud Resource & Information Management System (CRIMSy)
- * Copyright 2020 Leibniz-Institut f. Pflanzenbiochemie
+ * Copyright 2023 Leibniz-Institut f. Pflanzenbiochemie
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  * limitations under the License.
  *
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 import java.util.Date;
 import java.security.Key;

diff --git a/...e/lbac/device/job/TokenGeneratorTest.java → .../de/ipb_halle/job/TokenGeneratorTest.java b/...e/lbac/device/job/TokenGeneratorTest.java → .../de/ipb_halle/job/TokenGeneratorTest.java
@@ -15,7 +15,7 @@
  * limitations under the License.
  * 
  */
-package de.ipb_halle.lbac.device.job;
+package de.ipb_halle.job;
 
 
 import org.junit.Before;