Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Upgrade to JakartaEE 10 API for compatibility with Payara 6 #138

Merged
merged 14 commits into from
Aug 14, 2023
Merged

Upgrade to JakartaEE 10 API for compatibility with Payara 6 #138

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
28b2a01
Use python3
ajkyffin Sep 5, 2022
e6cc4a4
Upgrade to Java 11
ajkyffin Sep 5, 2022
34d3727
Upgrade to jakartaee-api 9.1.0
ajkyffin Sep 5, 2022
39bfbd5
Upgrade to jakartaee-api 10.0.0
ajkyffin Nov 10, 2022
40279ff
Merge branch 'master' into payara6
RKrahl Aug 3, 2023
5f40f66
Update schema in web.xml
ajkyffin Aug 3, 2023
50ab0ee
Update icat.client dependency to release version
ajkyffin Aug 4, 2023
1f5bd4c
Fix indentation error
ajkyffin Aug 7, 2023
5445d93
Use payara6 branch of icat-ansible in CI
ajkyffin Aug 7, 2023
ab9fdbb
Install lxml via apt on GitHub Actions
ajkyffin Aug 7, 2023
ddb620f
Update maven-war-plugin for compatibility with Java 17
ajkyffin Aug 8, 2023
5430c3a
Changes to GitHub Actions
ajkyffin Aug 8, 2023
9d192f6
Update release notes
RKrahl Aug 11, 2023
382d1d7
Merge branch 'master' into payara6
RKrahl Aug 14, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 7 additions & 11 deletions .github/workflows/ci-build.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,25 +8,18 @@ on:

jobs:
build_and_tests:
runs-on: ubuntu-20.04
runs-on: ubuntu-22.04
strategy:
fail-fast: false
matrix:
include:
- version: 8
java_version: [11, 17]

steps:
# Setup Java & Python
- name: Setup Java
uses: actions/setup-java@3f07048e3d294f56e9b90ac5ea2c6f74e9ad0f98 # v3.10.0
with:
distribution: 'temurin'
java-version: ${{ matrix.version }}
- name: Setup Python
uses: actions/setup-python@d27e3f3d7c64b4bbf8e4abfb9b63b83e846e0435 # v4.5.0
with:
python-version: "3.9.7"
architecture: x64
java-version: ${{ matrix.java_version }}

- name: Cache local Maven repository
uses: actions/cache@69d9d449aced6a2ede0bc19182fadc3a0a42d2b0 # v3.2.6
Expand All @@ -36,13 +29,16 @@ jobs:
restore-keys: |
${{ runner.os }}-maven-

- name: Run apt-get update
run: sudo apt-get update

# ICAT Ansible clone and install dependencies
- name: Checkout icat-ansible
uses: actions/checkout@ac593985615ec2ede58e132d2e21d2b1cbd6127c # v3.3.0
with:
repository: icatproject-contrib/icat-ansible
path: icat-ansible
ref: master
ref: payara6
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I guess that will need to be changed back to master as soon as icatproject-contrib/icat-ansible#84 gets merged.

- name: Install Ansible
run: pip install -r icat-ansible/requirements.txt

Expand Down
31 changes: 16 additions & 15 deletions pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@
<dependency>
<groupId>org.icatproject</groupId>
<artifactId>icat.client</artifactId>
<version>4.10.0</version>
<version>6.0.0</version>
</dependency>

<dependency>
Expand Down Expand Up @@ -102,9 +102,10 @@
</dependency>

<dependency>
<groupId>javax</groupId>
<artifactId>javaee-api</artifactId>
<version>7.0</version>
<groupId>jakarta.platform</groupId>
<artifactId>jakarta.jakartaee-api</artifactId>
<version>10.0.0</version>
<scope>provided</scope>
</dependency>

<dependency>
Expand All @@ -114,15 +115,16 @@
</dependency>

<dependency>
<groupId>commons-fileupload</groupId>
<artifactId>commons-fileupload</artifactId>
<version>1.5</version>
<groupId>com.sun.xml.ws</groupId>
<artifactId>jaxws-rt</artifactId>
<version>4.0.0</version>
<scope>test</scope>
</dependency>

<dependency>
<groupId>org.glassfish</groupId>
<artifactId>javax.json</artifactId>
<version>1.0.4</version>
<groupId>org.eclipse.parsson</groupId>
<artifactId>parsson</artifactId>
<version>1.1.0</version>
<scope>test</scope>
</dependency>

Expand Down Expand Up @@ -157,7 +159,7 @@
<plugin>
<groupId>com.qmino</groupId>
<artifactId>miredot-plugin</artifactId>
<version>1.6.2</version>
<version>2.4.1-Java11</version>
<executions>
<execution>
<id>miredot</id>
Expand Down Expand Up @@ -253,10 +255,9 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<version>3.10.1</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
<release>11</release>
</configuration>
</plugin>

Expand Down Expand Up @@ -308,7 +309,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<version>3.0.0</version>
<version>3.4.0</version>
</plugin>

<plugin>
Expand Down
10 changes: 5 additions & 5 deletions src/main/java/org/icatproject/ids/CORSResponseFilter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,11 @@

import java.io.IOException;

import javax.ws.rs.container.ContainerRequestContext;
import javax.ws.rs.container.ContainerResponseContext;
import javax.ws.rs.container.ContainerResponseFilter;
import javax.ws.rs.core.MultivaluedMap;
import javax.ws.rs.ext.Provider;
import jakarta.ws.rs.container.ContainerRequestContext;
import jakarta.ws.rs.container.ContainerResponseContext;
import jakarta.ws.rs.container.ContainerResponseFilter;
import jakarta.ws.rs.core.MultivaluedMap;
import jakarta.ws.rs.ext.Provider;

@Provider
public class CORSResponseFilter implements ContainerResponseFilter {
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/org/icatproject/ids/DataSelection.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@
import java.util.Map;
import java.util.Set;

import javax.json.Json;
import javax.json.JsonArray;
import javax.json.JsonValue;
import jakarta.json.Json;
import jakarta.json.JsonArray;
import jakarta.json.JsonValue;

import org.icatproject.Datafile;
import org.icatproject.Dataset;
Expand Down
10 changes: 5 additions & 5 deletions src/main/java/org/icatproject/ids/FileChecker.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,11 @@
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;

import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
import javax.ejb.EJB;
import javax.ejb.Singleton;
import javax.ejb.Startup;
import jakarta.annotation.PostConstruct;
import jakarta.annotation.PreDestroy;
import jakarta.ejb.EJB;
import jakarta.ejb.Singleton;
import jakarta.ejb.Startup;

import org.icatproject.Datafile;
import org.icatproject.Dataset;
Expand Down
14 changes: 7 additions & 7 deletions src/main/java/org/icatproject/ids/FiniteStateMachine.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,13 +20,13 @@
import java.util.UUID;
import java.util.concurrent.ConcurrentHashMap;

import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
import javax.ejb.DependsOn;
import javax.ejb.EJB;
import javax.ejb.Singleton;
import javax.json.Json;
import javax.json.stream.JsonGenerator;
import jakarta.annotation.PostConstruct;
import jakarta.annotation.PreDestroy;
import jakarta.ejb.DependsOn;
import jakarta.ejb.EJB;
import jakarta.ejb.Singleton;
import jakarta.json.Json;
import jakarta.json.stream.JsonGenerator;

import org.icatproject.Dataset;
import org.icatproject.ids.LockManager.Lock;
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/icatproject/ids/ICATGetter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import java.net.MalformedURLException;
import java.net.URL;

import javax.xml.ws.WebServiceException;
import jakarta.xml.ws.WebServiceException;

import org.icatproject.ICAT;
import org.icatproject.ICATService;
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/icatproject/ids/IcatReader.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@

import java.util.List;

import javax.annotation.PostConstruct;
import javax.ejb.Singleton;
import jakarta.annotation.PostConstruct;
import jakarta.ejb.Singleton;

import org.icatproject.EntityBaseBean;
import org.icatproject.ICAT;
Expand Down
22 changes: 11 additions & 11 deletions src/main/java/org/icatproject/ids/IdsBean.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,17 +40,17 @@
import java.util.zip.ZipException;
import java.util.zip.ZipOutputStream;

import javax.annotation.PostConstruct;
import javax.ejb.EJB;
import javax.ejb.Stateless;
import javax.json.Json;
import javax.json.JsonNumber;
import javax.json.JsonObject;
import javax.json.JsonReader;
import javax.json.JsonValue;
import javax.json.stream.JsonGenerator;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.StreamingOutput;
import jakarta.annotation.PostConstruct;
import jakarta.ejb.EJB;
import jakarta.ejb.Stateless;
import jakarta.json.Json;
import jakarta.json.JsonNumber;
import jakarta.json.JsonObject;
import jakarta.json.JsonReader;
import jakarta.json.JsonValue;
import jakarta.json.stream.JsonGenerator;
import jakarta.ws.rs.core.Response;
import jakarta.ws.rs.core.StreamingOutput;
import javax.xml.datatype.DatatypeFactory;

import org.icatproject.Datafile;
Expand Down
72 changes: 33 additions & 39 deletions src/main/java/org/icatproject/ids/IdsService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,35 +3,33 @@
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
import javax.ejb.EJB;
import javax.ejb.Stateless;
import javax.json.Json;
import javax.json.stream.JsonGenerator;
import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.Consumes;
import javax.ws.rs.DELETE;
import javax.ws.rs.FormParam;
import javax.ws.rs.GET;
import javax.ws.rs.HeaderParam;
import javax.ws.rs.POST;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;

import org.apache.commons.fileupload.FileItemIterator;
import org.apache.commons.fileupload.FileItemStream;
import org.apache.commons.fileupload.FileUploadException;
import org.apache.commons.fileupload.servlet.ServletFileUpload;
import org.apache.commons.fileupload.util.Streams;
import jakarta.annotation.PostConstruct;
import jakarta.annotation.PreDestroy;
import jakarta.ejb.EJB;
import jakarta.ejb.Stateless;
import jakarta.json.Json;
import jakarta.json.stream.JsonGenerator;
import jakarta.servlet.ServletException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.Part;
import jakarta.ws.rs.Consumes;
import jakarta.ws.rs.DELETE;
import jakarta.ws.rs.FormParam;
import jakarta.ws.rs.GET;
import jakarta.ws.rs.HeaderParam;
import jakarta.ws.rs.POST;
import jakarta.ws.rs.PUT;
import jakarta.ws.rs.Path;
import jakarta.ws.rs.Produces;
import jakarta.ws.rs.QueryParam;
import jakarta.ws.rs.core.Context;
import jakarta.ws.rs.core.MediaType;
import jakarta.ws.rs.core.Response;

import org.icatproject.ids.exceptions.BadRequestException;
import org.icatproject.ids.exceptions.DataNotOnlineException;
import org.icatproject.ids.exceptions.InsufficientPrivilegesException;
Expand Down Expand Up @@ -652,11 +650,7 @@ public Response put(@Context HttpServletRequest request, InputStream body,
@Produces(MediaType.APPLICATION_JSON)
public Response putAsPost(@Context HttpServletRequest request) throws BadRequestException, NotFoundException,
InternalException, InsufficientPrivilegesException, NotImplementedException, DataNotOnlineException {
if (!ServletFileUpload.isMultipartContent(request)) {
throw new BadRequestException("Multipart content expected");
}
try {
ServletFileUpload upload = new ServletFileUpload();
String sessionId = null;
String name = null;
String datafileFormatId = null;
Expand All @@ -670,13 +664,11 @@ public Response putAsPost(@Context HttpServletRequest request) throws BadRequest
boolean padding = false;

// Parse the request
FileItemIterator iter = upload.getItemIterator(request);
while (iter.hasNext()) {
FileItemStream item = iter.next();
String fieldName = item.getFieldName();
InputStream stream = item.openStream();
if (item.isFormField()) {
String value = Streams.asString(stream);
for (Part part : request.getParts()) {
String fieldName = part.getName();
InputStream stream = part.getInputStream();
if (part.getSubmittedFileName() == null) {
String value = new String(stream.readAllBytes(), StandardCharsets.UTF_8);
if (fieldName.equals("sessionId")) {
sessionId = value;
} else if (fieldName.equals("name")) {
Expand All @@ -702,15 +694,17 @@ public Response putAsPost(@Context HttpServletRequest request) throws BadRequest
}
} else {
if (name == null) {
name = item.getName();
name = part.getSubmittedFileName();
}
result = idsBean.put(stream, sessionId, name, datafileFormatId, datasetId, description, doi,
datafileCreateTime, datafileModTime, wrap, padding, request.getRemoteAddr());
}
}
return result;
} catch (IOException | FileUploadException e) {
} catch (IOException e) {
throw new InternalException(e.getClass() + " " + e.getMessage());
} catch (ServletException e) {
throw new BadRequestException("Multipart content expected");
}
}

Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/icatproject/ids/LockManager.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import javax.annotation.PostConstruct;
import javax.ejb.Singleton;
import jakarta.annotation.PostConstruct;
import jakarta.ejb.Singleton;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/icatproject/ids/PropertyHandler.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@
import java.util.Properties;
import java.util.Set;

import javax.json.Json;
import javax.json.JsonReader;
import jakarta.json.Json;
import jakarta.json.JsonReader;

import org.icatproject.ICAT;
import org.icatproject.IcatException_Exception;
Expand Down
10 changes: 5 additions & 5 deletions src/main/java/org/icatproject/ids/Tidier.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@
import java.util.Timer;
import java.util.TimerTask;

import javax.annotation.PostConstruct;
import javax.annotation.PreDestroy;
import javax.ejb.EJB;
import javax.ejb.Singleton;
import javax.ejb.Startup;
import jakarta.annotation.PostConstruct;
import jakarta.annotation.PreDestroy;
import jakarta.ejb.EJB;
import jakarta.ejb.Singleton;
import jakarta.ejb.Startup;

import org.icatproject.Datafile;
import org.icatproject.Dataset;
Expand Down
Loading