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Merge branch 'main' into main-seperate-logs-for-cli-jobs-fixing-corruption-of-log-file

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Jens Vannerum
2025-01-14 12:11:13 +01:00
parent 9f39a3d6a5 b85380452a
commit da73014ee6
196 changed files with 3031 additions and 2239 deletions
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118
.github/dependabot.yml vendored Normal file
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@@ -0,0 +1,118 @@
#-------------------
# DSpace's dependabot rules. Enables maven updates for all dependencies on a weekly basis
# for main and any maintenance branches. Security updates only apply to main.
#-------------------
version: 2
updates:
- package-ecosystem: "maven"
directory: "/"
schedule:
interval: "weekly"
# Allow up to 10 open PRs for dependencies
open-pull-requests-limit: 10
# Group together some upgrades in a single PR
groups:
# Group together all Build Tools in a single PR
build-tools:
applies-to: version-updates
patterns:
- "org.apache.maven.plugins:*"
- "*:*-maven-plugin"
- "*:maven-*-plugin"
- "com.github.spotbugs:spotbugs"
- "com.google.code.findbugs:*"
- "com.google.errorprone:*"
- "com.puppycrawl.tools:checkstyle"
- "org.sonatype.plugins:*"
exclude-patterns:
# Exclude anything from Spring, as that is in a separate group
- "org.springframework.*:*"
update-types:
- "minor"
- "patch"
test-tools:
applies-to: version-updates
patterns:
- "junit:*"
- "com.github.stefanbirker:system-rules"
- "com.h2database:*"
- "io.findify:s3mock*"
- "io.netty:*"
- "org.hamcrest:*"
- "org.mock-server:*"
- "org.mockito:*"
update-types:
- "minor"
- "patch"
# Group together all Apache Commons deps in a single PR
apache-commons:
applies-to: version-updates
patterns:
- "org.apache.commons:*"
- "commons-*:commons-*"
update-types:
- "minor"
- "patch"
# Group together all fasterxml deps in a single PR
fasterxml:
applies-to: version-updates
patterns:
- "com.fasterxml:*"
- "com.fasterxml.*:*"
update-types:
- "minor"
- "patch"
# Group together all Hibernate deps in a single PR
hibernate:
applies-to: version-updates
patterns:
- "org.hibernate.*:*"
update-types:
- "minor"
- "patch"
# Group together all Jakarta deps in a single PR
jakarta:
applies-to: version-updates
patterns:
- "jakarta.*:*"
- "org.eclipse.angus:jakarta.mail"
- "org.glassfish.jaxb:jaxb-runtime"
update-types:
- "minor"
- "patch"
# Group together all Google deps in a single PR
google-apis:
applies-to: version-updates
patterns:
- "com.google.apis:*"
- "com.google.api-client:*"
- "com.google.http-client:*"
- "com.google.oauth-client:*"
update-types:
- "minor"
- "patch"
# Group together all Spring deps in a single PR
spring:
applies-to: version-updates
patterns:
- "org.springframework:*"
- "org.springframework.*:*"
update-types:
- "minor"
- "patch"
# Group together all WebJARs deps in a single PR
webjars:
applies-to: version-updates
patterns:
- "org.webjars:*"
- "org.webjars.*:*"
update-types:
- "minor"
- "patch"
ignore:
# Don't try to auto-update any DSpace dependencies
- dependency-name: "org.dspace:*"
- dependency-name: "org.dspace.*:*"
# Ignore all major version updates for all dependencies. We'll only automate minor/patch updates.
- dependency-name: "*"
update-types: ["version-update:semver-major"]

101
.github/workflows/docker.yml vendored
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@@ -15,6 +15,7 @@ on:
permissions:
contents: read # to fetch code (actions/checkout)
packages: write # to write images to GitHub Container Registry (GHCR)
jobs:
####################################################
@@ -147,4 +148,102 @@ jobs:
tags_flavor: suffix=-loadsql
secrets:
DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
DOCKER_ACCESS_TOKEN: ${{ secrets.DOCKER_ACCESS_TOKEN }}
DOCKER_ACCESS_TOKEN: ${{ secrets.DOCKER_ACCESS_TOKEN }}
#################################################################################
# Test Deployment via Docker to ensure newly built images are working properly
#################################################################################
docker-deploy:
# Ensure this job never runs on forked repos. It's only executed for 'dspace/dspace'
if: github.repository == 'dspace/dspace'
runs-on: ubuntu-latest
# Must run after all major images are built
needs: [dspace, dspace-test, dspace-cli, dspace-postgres-pgcrypto, dspace-solr]
env:
# Override defaults dspace.server.url because backend starts at http://127.0.0.1:8080
dspace__P__server__P__url: http://127.0.0.1:8080/server
# Enable all optional modules / controllers for this test deployment.
# This helps check for errors in deploying these modules via Spring Boot
iiif__P__enabled: true
ldn__P__enabled: true
oai__P__enabled: true
rdf__P__enabled: true
signposting__P__enabled: true
sword__D__server__P__enabled: true
swordv2__D__server__P__enabled: true
# If this is a PR against main (default branch), use "latest".
# Else if this is a PR against a different branch, used the base branch name.
# Else if this is a commit on main (default branch), use the "latest" tag.
# Else, just use the branch name.
# NOTE: DSPACE_VER is used because our docker compose scripts default to using the "-test" image.
DSPACE_VER: ${{ (github.event_name == 'pull_request' && github.event.pull_request.base.ref == github.event.repository.default_branch && 'latest') || (github.event_name == 'pull_request' && github.event.pull_request.base.ref) || (github.ref_name == github.event.repository.default_branch && 'latest') || github.ref_name }}
# Docker Registry to use for Docker compose scripts below.
# We use GitHub's Container Registry to avoid aggressive rate limits at DockerHub.
DOCKER_REGISTRY: ghcr.io
steps:
# Checkout our codebase (to get access to Docker Compose scripts)
- name: Checkout codebase
uses: actions/checkout@v4
# Download Docker image artifacts (which were just built by reusable-docker-build.yml)
- name: Download Docker image artifacts
uses: actions/download-artifact@v4
with:
# Download all amd64 Docker images (TAR files) into the /tmp/docker directory
pattern: docker-image-*-linux-amd64
path: /tmp/docker
merge-multiple: true
# Load each of the images into Docker by calling "docker image load" for each.
# This ensures we are using the images just built & not any prior versions on DockerHub
- name: Load all downloaded Docker images
run: |
find /tmp/docker -type f -name "*.tar" -exec docker image load --input "{}" \;
docker image ls -a
# Start backend using our compose script in the codebase.
- name: Start backend in Docker
run: |
docker compose -f docker-compose.yml up -d
sleep 10
docker container ls
# Create a test admin account. Load test data from a simple set of AIPs as defined in cli.ingest.yml
- name: Load test data into Backend
run: |
docker compose -f docker-compose-cli.yml run --rm dspace-cli create-administrator -e test@test.edu -f admin -l user -p admin -c en
docker compose -f docker-compose-cli.yml -f dspace/src/main/docker-compose/cli.ingest.yml run --rm dspace-cli
# Verify backend started successfully.
# 1. Make sure root endpoint is responding (check for dspace.name defined in docker-compose.yml)
# 2. Also check /collections endpoint to ensure the test data loaded properly (check for a collection name in AIPs)
- name: Verify backend is responding properly
run: |
result=$(wget -O- -q http://127.0.0.1:8080/server/api)
echo "$result"
echo "$result" | grep -oE "\"DSpace Started with Docker Compose\","
result=$(wget -O- -q http://127.0.0.1:8080/server/api/core/collections)
echo "$result"
echo "$result" | grep -oE "\"Dog in Yard\","
# Verify Handle Server can be stared and is working properly
# 1. First generate the "[dspace]/handle-server" folder with the sitebndl.zip
# 2. Start the Handle Server (and wait 20 seconds to let it start up)
# 3. Verify logs do NOT include "Exception" in the text (as that means an error occurred)
# 4. Check that Handle Proxy HTML page is responding on default port (8000)
- name: Verify Handle Server is working properly
run: |
docker exec -i dspace /dspace/bin/make-handle-config
echo "Starting Handle Server..."
docker exec -i dspace /dspace/bin/start-handle-server
sleep 20
echo "Checking for errors in error.log"
result=$(docker exec -i dspace sh -c "cat /dspace/handle-server/logs/error.log* || echo ''")
echo "$result"
echo "$result" | grep -vqz "Exception"
echo "Checking for errors in handle-server.log..."
result=$(docker exec -i dspace cat /dspace/log/handle-server.log)
echo "$result"
echo "$result" | grep -vqz "Exception"
echo "Checking to see if Handle Proxy webpage is available..."
result=$(wget -O- -q http://127.0.0.1:8000/)
echo "$result"
echo "$result" | grep -oE "Handle Proxy"
# Shutdown our containers
- name: Shutdown Docker containers
run: |
docker compose -f docker-compose.yml down

225
.github/workflows/reusable-docker-build.yml vendored
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@@ -54,10 +54,13 @@ env:
# For a new commit on default branch (main), use the literal tag 'latest' on Docker image.
# For a new commit on other branches, use the branch name as the tag for Docker image.
# For a new tag, copy that tag name as the tag for Docker image.
# For a pull request, use the name of the base branch that the PR was created against or "latest" (for main).
# e.g. PR against 'main' will use "latest". a PR against 'dspace-7_x' will use 'dspace-7_x'.
IMAGE_TAGS: |
type=raw,value=latest,enable=${{ github.ref_name == github.event.repository.default_branch }}
type=ref,event=branch,enable=${{ github.ref_name != github.event.repository.default_branch }}
type=ref,event=tag
type=raw,value=${{ (github.event.pull_request.base.ref == github.event.repository.default_branch && 'latest') || github.event.pull_request.base.ref }},enable=${{ github.event_name == 'pull_request' }}
# Define default tag "flavor" for docker/metadata-action per
# https://github.com/docker/metadata-action#flavor-input
# We manage the 'latest' tag ourselves to the 'main' branch (see settings above)
@@ -72,6 +75,9 @@ env:
DEPLOY_DEMO_BRANCH: 'dspace-8_x'
DEPLOY_SANDBOX_BRANCH: 'main'
DEPLOY_ARCH: 'linux/amd64'
# Registry used during building of Docker images. (All images are later copied to docker.io registry)
# We use GitHub's Container Registry to avoid aggressive rate limits at DockerHub.
DOCKER_BUILD_REGISTRY: ghcr.io
jobs:
docker-build:
@@ -96,6 +102,7 @@ jobs:
# This step converts the slashes in the "arch" matrix values above into dashes & saves to env.ARCH_NAME
# E.g. "linux/amd64" becomes "linux-amd64"
# This is necessary because all upload artifacts CANNOT have special chars (like slashes)
# NOTE: The regex-like syntax below is Bash Parameter Substitution
- name: Prepare
run: |
platform=${{ matrix.arch }}
@@ -105,35 +112,45 @@ jobs:
- name: Checkout codebase
uses: actions/checkout@v4
# https://github.com/docker/setup-buildx-action
- name: Setup Docker Buildx
uses: docker/setup-buildx-action@v3
# https://github.com/docker/login-action
# NOTE: This login occurs for BOTH non-PRs or PRs. PRs *must* also login to access private images from GHCR
# during the build process
- name: Login to ${{ env.DOCKER_BUILD_REGISTRY }}
uses: docker/login-action@v3
with:
registry: ${{ env.DOCKER_BUILD_REGISTRY }}
username: ${{ github.repository_owner }}
password: ${{ secrets.GITHUB_TOKEN }}
# https://github.com/docker/setup-qemu-action
- name: Set up QEMU emulation to build for multiple architectures
uses: docker/setup-qemu-action@v3
# https://github.com/docker/login-action
- name: Login to DockerHub
# Only login if not a PR, as PRs only trigger a Docker build and not a push
if: ${{ ! matrix.isPr }}
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_ACCESS_TOKEN }}
# https://github.com/docker/setup-buildx-action
- name: Setup Docker Buildx
uses: docker/setup-buildx-action@v3
# https://github.com/docker/metadata-action
# Get Metadata for docker_build_deps step below
- name: Sync metadata (tags, labels) from GitHub to Docker for image
# Extract metadata used for Docker images in all build steps below
- name: Extract metadata (tags, labels) from GitHub for Docker image
id: meta_build
uses: docker/metadata-action@v5
with:
images: ${{ env.IMAGE_NAME }}
images: ${{ env.DOCKER_BUILD_REGISTRY }}/${{ env.IMAGE_NAME }}
tags: ${{ env.IMAGE_TAGS }}
flavor: ${{ env.TAGS_FLAVOR }}
#--------------------------------------------------------------------
# First, for all branch commits (non-PRs) we build the image & upload
# to GitHub Container Registry (GHCR). After uploading the image
# to GHCR, we store the image digest in an artifact, so we can
# create a merged manifest later (see 'docker-build_manifest' job).
#
# NOTE: We use GHCR in order to avoid aggressive rate limits at DockerHub.
#--------------------------------------------------------------------
# https://github.com/docker/build-push-action
- name: Build and push image
- name: Build and push image to ${{ env.DOCKER_BUILD_REGISTRY }}
if: ${{ ! matrix.isPr }}
id: docker_build
uses: docker/build-push-action@v5
with:
@@ -141,15 +158,20 @@ jobs:
${{ inputs.dockerfile_additional_contexts }}
context: ${{ inputs.dockerfile_context }}
file: ${{ inputs.dockerfile_path }}
# Tell DSpace's Docker files to use the build registry instead of DockerHub
build-args:
DOCKER_REGISTRY=${{ env.DOCKER_BUILD_REGISTRY }}
platforms: ${{ matrix.arch }}
# For pull requests, we run the Docker build (to ensure no PR changes break the build),
# but we ONLY do an image push to DockerHub if it's NOT a PR
push: ${{ ! matrix.isPr }}
push: true
# Use tags / labels provided by 'docker/metadata-action' above
tags: ${{ steps.meta_build.outputs.tags }}
labels: ${{ steps.meta_build.outputs.labels }}
# Use GitHub cache to load cached Docker images and cache the results of this build
# This decreases the number of images we need to fetch from DockerHub
cache-from: type=gha,scope=${{ inputs.build_id }}
cache-to: type=gha,scope=${{ inputs.build_id }},mode=max
# Export the digest of Docker build locally (for non PRs only)
# Export the digest of Docker build locally
- name: Export Docker build digest
if: ${{ ! matrix.isPr }}
run: |
@@ -157,7 +179,8 @@ jobs:
digest="${{ steps.docker_build.outputs.digest }}"
touch "/tmp/digests/${digest#sha256:}"
# Upload digest to an artifact, so that it can be used in manifest below
# Upload digest to an artifact, so that it can be used in combined manifest below
# (The purpose of the combined manifest is to list both amd64 and arm64 builds under same tag)
- name: Upload Docker build digest to artifact
if: ${{ ! matrix.isPr }}
uses: actions/upload-artifact@v4
@@ -167,33 +190,60 @@ jobs:
if-no-files-found: error
retention-days: 1
# If this build is NOT a PR and passed in a REDEPLOY_SANDBOX_URL secret,
# Then redeploy https://sandbox.dspace.org if this build is for our deployment architecture and 'main' branch.
- name: Redeploy sandbox.dspace.org (based on main branch)
if: |
!matrix.isPR &&
env.REDEPLOY_SANDBOX_URL != '' &&
matrix.arch == env.DEPLOY_ARCH &&
github.ref_name == env.DEPLOY_SANDBOX_BRANCH
run: |
curl -X POST $REDEPLOY_SANDBOX_URL
#------------------------------------------------------------------------------
# Second, we build the image again in order to store it in a local TAR file.
# This TAR of the image is cached/saved as an artifact, so that it can be used
# by later jobs to install the brand-new images for automated testing.
# This TAR build is performed BOTH for PRs and for branch commits (non-PRs).
#
# (This approach has the advantage of avoiding having to download the newly built
# image from DockerHub or GHCR during automated testing.)
#
# See the 'docker-deploy' job in docker.yml as an example of where this TAR is used.
#-------------------------------------------------------------------------------
# Build local image (again) and store in a TAR file in /tmp directory
# This step is only done for AMD64, as that's the only image we use in our automated testing (at this time).
# NOTE: This step cannot be combined with the build above as it's a different type of output.
- name: Build and push image to local TAR file
if: ${{ matrix.arch == 'linux/amd64'}}
uses: docker/build-push-action@v5
with:
build-contexts: |
${{ inputs.dockerfile_additional_contexts }}
context: ${{ inputs.dockerfile_context }}
file: ${{ inputs.dockerfile_path }}
# Tell DSpace's Docker files to use the build registry instead of DockerHub
build-args:
DOCKER_REGISTRY=${{ env.DOCKER_BUILD_REGISTRY }}
platforms: ${{ matrix.arch }}
tags: ${{ steps.meta_build.outputs.tags }}
labels: ${{ steps.meta_build.outputs.labels }}
# Use GitHub cache to load cached Docker images and cache the results of this build
# This decreases the number of images we need to fetch from DockerHub
cache-from: type=gha,scope=${{ inputs.build_id }}
cache-to: type=gha,scope=${{ inputs.build_id }},mode=max
# Export image to a local TAR file
outputs: type=docker,dest=/tmp/${{ inputs.build_id }}.tar
# If this build is NOT a PR and passed in a REDEPLOY_DEMO_URL secret,
# Then redeploy https://demo.dspace.org if this build is for our deployment architecture and demo branch.
- name: Redeploy demo.dspace.org (based on maintenance branch)
if: |
!matrix.isPR &&
env.REDEPLOY_DEMO_URL != '' &&
matrix.arch == env.DEPLOY_ARCH &&
github.ref_name == env.DEPLOY_DEMO_BRANCH
run: |
curl -X POST $REDEPLOY_DEMO_URL
# Upload the local docker image (in TAR file) to a build Artifact
# This step is only done for AMD64, as that's the only image we use in our automated testing (at this time).
- name: Upload local image TAR to artifact
if: ${{ matrix.arch == 'linux/amd64'}}
uses: actions/upload-artifact@v4
with:
name: docker-image-${{ inputs.build_id }}-${{ env.ARCH_NAME }}
path: /tmp/${{ inputs.build_id }}.tar
if-no-files-found: error
retention-days: 1
# Merge Docker digests (from various architectures) into a manifest.
# This runs after all Docker builds complete above, and it tells hub.docker.com
# that these builds should be all included in the manifest for this tag.
# (e.g. AMD64 and ARM64 should be listed as options under the same tagged Docker image)
##########################################################################################
# Merge Docker digests (from various architectures) into a single manifest.
# This runs after all Docker builds complete above. The purpose is to include all builds
# under a single manifest for this tag.
# (e.g. both linux/amd64 and linux/arm64 should be listed under the same tagged Docker image)
##########################################################################################
docker-build_manifest:
# Only run if this is NOT a PR
if: ${{ github.event_name != 'pull_request' }}
runs-on: ubuntu-latest
needs:
@@ -207,29 +257,102 @@ jobs:
pattern: digests-${{ inputs.build_id }}-*
merge-multiple: true
- name: Login to ${{ env.DOCKER_BUILD_REGISTRY }}
uses: docker/login-action@v3
with:
registry: ${{ env.DOCKER_BUILD_REGISTRY }}
username: ${{ github.repository_owner }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Add Docker metadata for image
id: meta
uses: docker/metadata-action@v5
with:
images: ${{ env.DOCKER_BUILD_REGISTRY }}/${{ env.IMAGE_NAME }}
tags: ${{ env.IMAGE_TAGS }}
flavor: ${{ env.TAGS_FLAVOR }}
- name: Create manifest list from digests and push to ${{ env.DOCKER_BUILD_REGISTRY }}
working-directory: /tmp/digests
run: |
docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
$(printf '${{ env.DOCKER_BUILD_REGISTRY }}/${{ env.IMAGE_NAME }}@sha256:%s ' *)
- name: Inspect manifest in ${{ env.DOCKER_BUILD_REGISTRY }}
run: |
docker buildx imagetools inspect ${{ env.DOCKER_BUILD_REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}
##########################################################################################
# Copy images / manifest to DockerHub.
# This MUST run after *both* images (AMD64 and ARM64) are built and uploaded to GitHub
# Container Registry (GHCR). Attempting to run this in parallel to GHCR builds can result
# in a race condition...i.e. the copy to DockerHub may fail if GHCR image has been updated
# at the moment when the copy occurs.
##########################################################################################
docker-copy_to_dockerhub:
# Only run if this is NOT a PR
if: ${{ github.event_name != 'pull_request' }}
runs-on: ubuntu-latest
needs:
- docker-build_manifest
steps:
# 'regctl' is used to more easily copy the image to DockerHub and obtain the digest from DockerHub
# See https://github.com/regclient/regclient/blob/main/docs/regctl.md
- name: Install regctl for Docker registry tools
uses: regclient/actions/regctl-installer@main
with:
release: 'v0.8.0'
# This recreates Docker tags for DockerHub
- name: Add Docker metadata for image
id: meta_dockerhub
uses: docker/metadata-action@v5
with:
images: ${{ env.IMAGE_NAME }}
tags: ${{ env.IMAGE_TAGS }}
flavor: ${{ env.TAGS_FLAVOR }}
- name: Login to Docker Hub
# Login to source registry first, as this is where we are copying *from*
- name: Login to ${{ env.DOCKER_BUILD_REGISTRY }}
uses: docker/login-action@v3
with:
registry: ${{ env.DOCKER_BUILD_REGISTRY }}
username: ${{ github.repository_owner }}
password: ${{ secrets.GITHUB_TOKEN }}
# Login to DockerHub, since this is where we are copying *to*
- name: Login to DockerHub
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_ACCESS_TOKEN }}
- name: Create manifest list from digests and push
working-directory: /tmp/digests
# Copy the image from source to DockerHub
- name: Copy image from ${{ env.DOCKER_BUILD_REGISTRY }} to docker.io
run: |
docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \
$(printf '${{ env.IMAGE_NAME }}@sha256:%s ' *)
regctl image copy ${{ env.DOCKER_BUILD_REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.meta_dockerhub.outputs.version }} docker.io/${{ env.IMAGE_NAME }}:${{ steps.meta_dockerhub.outputs.version }}
- name: Inspect image
#--------------------------------------------------------------------
# Finally, check whether demo.dspace.org or sandbox.dspace.org need
# to be redeployed based on these new DockerHub images.
#--------------------------------------------------------------------
# If this build is for the branch that Sandbox uses and passed in a REDEPLOY_SANDBOX_URL secret,
# Then redeploy https://sandbox.dspace.org
- name: Redeploy sandbox.dspace.org (based on main branch)
if: |
env.REDEPLOY_SANDBOX_URL != '' &&
github.ref_name == env.DEPLOY_SANDBOX_BRANCH
run: |
docker buildx imagetools inspect ${{ env.IMAGE_NAME }}:${{ steps.meta.outputs.version }}
curl -X POST $REDEPLOY_SANDBOX_URL
# If this build is for the branch that Demo uses and passed in a REDEPLOY_DEMO_URL secret,
# Then redeploy https://demo.dspace.org
- name: Redeploy demo.dspace.org (based on maintenance branch)
if: |
env.REDEPLOY_DEMO_URL != '' &&
github.ref_name == env.DEPLOY_DEMO_BRANCH
run: |
curl -X POST $REDEPLOY_DEMO_URL

1
.gitignore vendored
View File

@@ -10,6 +10,7 @@ tags
.project
.classpath
.checkstyle
.factorypath
## Ignore project files created by IntelliJ IDEA
*.iml

35
Dockerfile
View File

@@ -6,10 +6,14 @@
# This Dockerfile uses JDK17 by default.
# To build with other versions, use "--build-arg JDK_VERSION=[value]"
ARG JDK_VERSION=17
# The Docker version tag to build from
ARG DSPACE_VERSION=latest
# The Docker registry to use for DSpace images. Defaults to "docker.io"
# NOTE: non-DSpace images are hardcoded to use "docker.io" and are not impacted by this build argument
ARG DOCKER_REGISTRY=docker.io
# Step 1 - Run Maven Build
FROM dspace/dspace-dependencies:${DSPACE_VERSION} AS build
FROM ${DOCKER_REGISTRY}/dspace/dspace-dependencies:${DSPACE_VERSION} AS build
ARG TARGET_DIR=dspace-installer
WORKDIR /app
# The dspace-installer directory will be written to /install
@@ -31,35 +35,38 @@ RUN mvn --no-transfer-progress package ${MAVEN_FLAGS} && \
RUN rm -rf /install/webapps/server/
# Step 2 - Run Ant Deploy
FROM eclipse-temurin:${JDK_VERSION} AS ant_build
FROM docker.io/eclipse-temurin:${JDK_VERSION} AS ant_build
ARG TARGET_DIR=dspace-installer
# COPY the /install directory from 'build' container to /dspace-src in this container
COPY --from=build /install /dspace-src
WORKDIR /dspace-src
# Create the initial install deployment using ANT
ENV ANT_VERSION 1.10.13
ENV ANT_HOME /tmp/ant-$ANT_VERSION
ENV PATH $ANT_HOME/bin:$PATH
# Need wget to install ant
RUN apt-get update \
&& apt-get install -y --no-install-recommends wget \
&& apt-get purge -y --auto-remove \
&& rm -rf /var/lib/apt/lists/*
ENV ANT_VERSION=1.10.13
ENV ANT_HOME=/tmp/ant-$ANT_VERSION
ENV PATH=$ANT_HOME/bin:$PATH
# Download and install 'ant'
RUN mkdir $ANT_HOME && \
wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
curl --silent --show-error --location --fail --retry 5 --output /tmp/apache-ant.tar.gz \
https://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz && \
tar -zx --strip-components=1 -f /tmp/apache-ant.tar.gz -C $ANT_HOME && \
rm /tmp/apache-ant.tar.gz
# Run necessary 'ant' deploy scripts
RUN ant init_installation update_configs update_code update_webapps
# Step 3 - Start up DSpace via Runnable JAR
FROM eclipse-temurin:${JDK_VERSION}
FROM docker.io/eclipse-temurin:${JDK_VERSION}
# NOTE: DSPACE_INSTALL must align with the "dspace.dir" default configuration.
ENV DSPACE_INSTALL=/dspace
# Copy the /dspace directory from 'ant_build' container to /dspace in this container
COPY --from=ant_build /dspace $DSPACE_INSTALL
WORKDIR $DSPACE_INSTALL
# Expose Tomcat port
EXPOSE 8080
# Need host command for "[dspace]/bin/make-handle-config"
RUN apt-get update \
&& apt-get install -y --no-install-recommends host \
&& apt-get purge -y --auto-remove \
&& rm -rf /var/lib/apt/lists/*
# Expose Tomcat port (8080) & Handle Server HTTP port (8000)
EXPOSE 8080 8000
# Give java extra memory (2GB)
ENV JAVA_OPTS=-Xmx2000m
# On startup, run DSpace Runnable JAR

26
Dockerfile.cli
View File

@@ -6,10 +6,14 @@
# This Dockerfile uses JDK17 by default.
# To build with other versions, use "--build-arg JDK_VERSION=[value]"
ARG JDK_VERSION=17
# The Docker version tag to build from
ARG DSPACE_VERSION=latest
# The Docker registry to use for DSpace images. Defaults to "docker.io"
# NOTE: non-DSpace images are hardcoded to use "docker.io" and are not impacted by this build argument
ARG DOCKER_REGISTRY=docker.io
# Step 1 - Run Maven Build
FROM dspace/dspace-dependencies:${DSPACE_VERSION} AS build
FROM ${DOCKER_REGISTRY}/dspace/dspace-dependencies:${DSPACE_VERSION} AS build
ARG TARGET_DIR=dspace-installer
WORKDIR /app
# The dspace-installer directory will be written to /install
@@ -25,28 +29,26 @@ RUN mvn --no-transfer-progress package && \
mvn clean
# Step 2 - Run Ant Deploy
FROM eclipse-temurin:${JDK_VERSION} AS ant_build
FROM docker.io/eclipse-temurin:${JDK_VERSION} AS ant_build
ARG TARGET_DIR=dspace-installer
# COPY the /install directory from 'build' container to /dspace-src in this container
COPY --from=build /install /dspace-src
WORKDIR /dspace-src
# Create the initial install deployment using ANT
ENV ANT_VERSION 1.10.13
ENV ANT_HOME /tmp/ant-$ANT_VERSION
ENV PATH $ANT_HOME/bin:$PATH
# Need wget to install ant
RUN apt-get update \
&& apt-get install -y --no-install-recommends wget \
&& apt-get purge -y --auto-remove \
&& rm -rf /var/lib/apt/lists/*
ENV ANT_VERSION=1.10.13
ENV ANT_HOME=/tmp/ant-$ANT_VERSION
ENV PATH=$ANT_HOME/bin:$PATH
# Download and install 'ant'
RUN mkdir $ANT_HOME && \
wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
curl --silent --show-error --location --fail --retry 5 --output /tmp/apache-ant.tar.gz \
https://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz && \
tar -zx --strip-components=1 -f /tmp/apache-ant.tar.gz -C $ANT_HOME && \
rm /tmp/apache-ant.tar.gz
# Run necessary 'ant' deploy scripts
RUN ant init_installation update_configs update_code
# Step 3 - Run jdk
FROM eclipse-temurin:${JDK_VERSION}
FROM docker.io/eclipse-temurin:${JDK_VERSION}
# NOTE: DSPACE_INSTALL must align with the "dspace.dir" default configuration.
ENV DSPACE_INSTALL=/dspace
# Copy the /dspace directory from 'ant_build' container to /dspace in this container

60
Dockerfile.dependencies
View File

@@ -6,8 +6,8 @@
# To build with other versions, use "--build-arg JDK_VERSION=[value]"
ARG JDK_VERSION=17
# Step 1 - Run Maven Build
FROM maven:3-eclipse-temurin-${JDK_VERSION} AS build
# Step 1 - Download all Dependencies
FROM docker.io/maven:3-eclipse-temurin-${JDK_VERSION} AS build
ARG TARGET_DIR=dspace-installer
WORKDIR /app
# Create the 'dspace' user account & home directory
@@ -19,16 +19,60 @@ RUN chown -Rv dspace: /app
# Switch to dspace user & run below commands as that user
USER dspace
# Copy the DSpace source code (from local machine) into the workdir (excluding .dockerignore contents)
ADD --chown=dspace . /app/
# This next part may look odd, but it speeds up the build of this image *significantly*.
# Copy ONLY the POMs to this image (from local machine). This will allow us to download all dependencies *without*
# performing any code compilation steps.
# Parent POM
ADD --chown=dspace pom.xml /app/
RUN mkdir -p /app/dspace
# 'dspace' module POM. Includes 'additions' ONLY, as it's the only submodule that is required to exist.
ADD --chown=dspace dspace/pom.xml /app/dspace/
RUN mkdir -p /app/dspace/modules/
ADD --chown=dspace dspace/modules/pom.xml /app/dspace/modules/
RUN mkdir -p /app/dspace/modules/additions
ADD --chown=dspace dspace/modules/additions/pom.xml /app/dspace/modules/additions/
# 'dspace-api' module POM
RUN mkdir -p /app/dspace-api
ADD --chown=dspace dspace-api/pom.xml /app/dspace-api/
# 'dspace-iiif' module POM
RUN mkdir -p /app/dspace-iiif
ADD --chown=dspace dspace-iiif/pom.xml /app/dspace-iiif/
# 'dspace-oai' module POM
RUN mkdir -p /app/dspace-oai
ADD --chown=dspace dspace-oai/pom.xml /app/dspace-oai/
# 'dspace-rdf' module POM
RUN mkdir -p /app/dspace-rdf
ADD --chown=dspace dspace-rdf/pom.xml /app/dspace-rdf/
# 'dspace-server-webapp' module POM
RUN mkdir -p /app/dspace-server-webapp
ADD --chown=dspace dspace-server-webapp/pom.xml /app/dspace-server-webapp/
# 'dspace-services' module POM
RUN mkdir -p /app/dspace-services
ADD --chown=dspace dspace-services/pom.xml /app/dspace-services/
# 'dspace-sword' module POM
RUN mkdir -p /app/dspace-sword
ADD --chown=dspace dspace-sword/pom.xml /app/dspace-sword/
# 'dspace-swordv2' module POM
RUN mkdir -p /app/dspace-swordv2
ADD --chown=dspace dspace-swordv2/pom.xml /app/dspace-swordv2/
# Trigger the installation of all maven dependencies (hide download progress messages)
# Maven flags here ensure that we skip final assembly, skip building test environment and skip all code verification checks.
# These flags speed up this installation as much as reasonably possible.
ENV MAVEN_FLAGS="-P-assembly -P-test-environment -Denforcer.skip=true -Dcheckstyle.skip=true -Dlicense.skip=true -Dxml.skip=true"
RUN mvn --no-transfer-progress install ${MAVEN_FLAGS}
# These flags speed up this installation and skip tasks we cannot perform as we don't have the full source code.
ENV MAVEN_FLAGS="-P-assembly -P-test-environment -Denforcer.skip=true -Dcheckstyle.skip=true -Dlicense.skip=true -Dxjc.skip=true -Dxml.skip=true"
RUN mvn --no-transfer-progress verify ${MAVEN_FLAGS}
# Clear the contents of the /app directory (including all maven builds), so no artifacts remain.
# Clear the contents of the /app directory (including all maven target folders), so no artifacts remain.
# This ensures when dspace:dspace is built, it will use the Maven local cache (~/.m2) for dependencies
USER root
RUN rm -rf /app/*

31
Dockerfile.test
View File

@@ -8,10 +8,14 @@
# This Dockerfile uses JDK17 by default.
# To build with other versions, use "--build-arg JDK_VERSION=[value]"
ARG JDK_VERSION=17
# The Docker version tag to build from
ARG DSPACE_VERSION=latest
# The Docker registry to use for DSpace images. Defaults to "docker.io"
# NOTE: non-DSpace images are hardcoded to use "docker.io" and are not impacted by this build argument
ARG DOCKER_REGISTRY=docker.io
# Step 1 - Run Maven Build
FROM dspace/dspace-dependencies:${DSPACE_VERSION} AS build
FROM ${DOCKER_REGISTRY}/dspace/dspace-dependencies:${DSPACE_VERSION} AS build
ARG TARGET_DIR=dspace-installer
WORKDIR /app
# The dspace-installer directory will be written to /install
@@ -30,33 +34,36 @@ RUN mvn --no-transfer-progress package && \
RUN rm -rf /install/webapps/server/
# Step 2 - Run Ant Deploy
FROM eclipse-temurin:${JDK_VERSION} AS ant_build
FROM docker.io/eclipse-temurin:${JDK_VERSION} AS ant_build
ARG TARGET_DIR=dspace-installer
# COPY the /install directory from 'build' container to /dspace-src in this container
COPY --from=build /install /dspace-src
WORKDIR /dspace-src
# Create the initial install deployment using ANT
ENV ANT_VERSION 1.10.12
ENV ANT_HOME /tmp/ant-$ANT_VERSION
ENV PATH $ANT_HOME/bin:$PATH
# Need wget to install ant
RUN apt-get update \
&& apt-get install -y --no-install-recommends wget \
&& apt-get purge -y --auto-remove \
&& rm -rf /var/lib/apt/lists/*
ENV ANT_VERSION=1.10.12
ENV ANT_HOME=/tmp/ant-$ANT_VERSION
ENV PATH=$ANT_HOME/bin:$PATH
# Download and install 'ant'
RUN mkdir $ANT_HOME && \
wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
curl --silent --show-error --location --fail --retry 5 --output /tmp/apache-ant.tar.gz \
https://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz && \
tar -zx --strip-components=1 -f /tmp/apache-ant.tar.gz -C $ANT_HOME && \
rm /tmp/apache-ant.tar.gz
# Run necessary 'ant' deploy scripts
RUN ant init_installation update_configs update_code update_webapps
# Step 3 - Start up DSpace via Runnable JAR
FROM eclipse-temurin:${JDK_VERSION}
FROM docker.io/eclipse-temurin:${JDK_VERSION}
# NOTE: DSPACE_INSTALL must align with the "dspace.dir" default configuration.
ENV DSPACE_INSTALL=/dspace
# Copy the /dspace directory from 'ant_build' container to /dspace in this container
COPY --from=ant_build /dspace $DSPACE_INSTALL
WORKDIR $DSPACE_INSTALL
# Need host command for "[dspace]/bin/make-handle-config"
RUN apt-get update \
&& apt-get install -y --no-install-recommends host \
&& apt-get purge -y --auto-remove \
&& rm -rf /var/lib/apt/lists/*
# Expose Tomcat port and debugging port
EXPOSE 8080 8000
# Give java extra memory (2GB)

2
checkstyle.xml
View File

@@ -92,7 +92,7 @@ For more information on CheckStyle configurations below, see: http://checkstyle.
<!-- Requirements for Javadocs for methods -->
<module name="JavadocMethod">
<!-- All public methods MUST HAVE Javadocs -->
<property name="scope" value="public"/>
<property name="accessModifiers" value="public"/>
<!-- Allow params, throws and return tags to be optional -->
<property name="allowMissingParamTags" value="true"/>
<property name="allowMissingReturnTag" value="true"/>

2
docker-compose-cli.yml
View File

@@ -6,7 +6,7 @@ networks:
external: true
services:
dspace-cli:
image: "${DOCKER_OWNER:-dspace}/dspace-cli:${DSPACE_VER:-latest}"
image: "${DOCKER_REGISTRY:-docker.io}/${DOCKER_OWNER:-dspace}/dspace-cli:${DSPACE_VER:-latest}"
container_name: dspace-cli
build:
context: .

6
docker-compose.yml
View File

@@ -28,7 +28,7 @@ services:
# from the host machine. This IP range MUST correspond to the 'dspacenet' subnet defined above.
proxies__P__trusted__P__ipranges: '172.23.0'
LOGGING_CONFIG: /dspace/config/log4j2-container.xml
image: "${DOCKER_OWNER:-dspace}/dspace:${DSPACE_VER:-latest-test}"
image: "${DOCKER_REGISTRY:-docker.io}/${DOCKER_OWNER:-dspace}/dspace:${DSPACE_VER:-latest-test}"
build:
context: .
dockerfile: Dockerfile.test
@@ -64,7 +64,7 @@ services:
dspacedb:
container_name: dspacedb
# Uses a custom Postgres image with pgcrypto installed
image: "${DOCKER_OWNER:-dspace}/dspace-postgres-pgcrypto:${DSPACE_VER:-latest}"
image: "${DOCKER_REGISTRY:-docker.io}/${DOCKER_OWNER:-dspace}/dspace-postgres-pgcrypto:${DSPACE_VER:-latest}"
build:
# Must build out of subdirectory to have access to install script for pgcrypto
context: ./dspace/src/main/docker/dspace-postgres-pgcrypto/
@@ -84,7 +84,7 @@ services:
# DSpace Solr container
dspacesolr:
container_name: dspacesolr
image: "${DOCKER_OWNER:-dspace}/dspace-solr:${DSPACE_VER:-latest}"
image: "${DOCKER_REGISTRY:-docker.io}/${DOCKER_OWNER:-dspace}/dspace-solr:${DSPACE_VER:-latest}"
build:
context: ./dspace/src/main/docker/dspace-solr/
# Provide path to Solr configs necessary to build Docker image

129
dspace-api/pom.xml
View File

@@ -102,7 +102,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<version>3.4.0</version>
<version>3.6.0</version>
<executions>
<execution>
<phase>validate</phase>
@@ -116,7 +116,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>buildnumber-maven-plugin</artifactId>
<version>3.2.0</version>
<version>3.2.1</version>
<configuration>
<revisionOnScmFailure>UNKNOWN_REVISION</revisionOnScmFailure>
</configuration>
@@ -177,7 +177,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>jaxb2-maven-plugin</artifactId>
<version>3.1.0</version>
<version>3.2.0</version>
<executions>
<execution>
<id>workflow-curation</id>
@@ -341,6 +341,14 @@
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j2-impl</artifactId>
</dependency>
<dependency>
<groupId>org.hibernate.orm</groupId>
<artifactId>hibernate-core</artifactId>
@@ -388,6 +396,13 @@
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-orm</artifactId>
<exclusions>
<!-- Spring JCL is unnecessary and conflicts with commons-logging when both are on classpath -->
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@@ -406,6 +421,16 @@
<groupId>org.mortbay.jasper</groupId>
<artifactId>apache-jsp</artifactId>
</exclusion>
<!-- Excluded BouncyCastle dependencies because we use a later version of BouncyCastle.
Having two versions of BouncyCastle in the classpath can cause Handle Server to throw errors. -->
<exclusion>
<groupId>org.bouncycastle</groupId>
<artifactId>bcpkix-jdk15on</artifactId>
</exclusion>
<exclusion>
<groupId>org.bouncycastle</groupId>
<artifactId>bcprov-jdk15on</artifactId>
</exclusion>
</exclusions>
</dependency>
@@ -623,7 +648,7 @@
<dependency>
<groupId>dnsjava</groupId>
<artifactId>dnsjava</artifactId>
<version>3.6.0</version>
<version>3.6.2</version>
</dependency>
<dependency>
@@ -672,22 +697,6 @@
<groupId>com.google.apis</groupId>
<artifactId>google-api-services-analytics</artifactId>
</dependency>
<dependency>
<groupId>com.google.api-client</groupId>
<artifactId>google-api-client</artifactId>
</dependency>
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client</artifactId>
</dependency>
<dependency>
<groupId>com.google.http-client</groupId>
<artifactId>google-http-client-jackson2</artifactId>
</dependency>
<dependency>
<groupId>com.google.oauth-client</groupId>
<artifactId>google-oauth-client</artifactId>
</dependency>
<!-- FindBugs -->
<dependency>
@@ -702,7 +711,6 @@
<dependency>
<groupId>jakarta.inject</groupId>
<artifactId>jakarta.inject-api</artifactId>
<version>2.0.1</version>
</dependency>
<!-- JAXB API and implementation (no longer bundled as of Java 11) -->
@@ -733,7 +741,7 @@
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk-s3</artifactId>
<version>1.12.261</version>
<version>1.12.779</version>
</dependency>
<!-- TODO: This may need to be replaced with the "orcid-model" artifact once this ticket is resolved:
@@ -776,18 +784,20 @@
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity-engine-core</artifactId>
<version>2.4.1</version>
</dependency>
<dependency>
<groupId>org.xmlunit</groupId>
<artifactId>xmlunit-core</artifactId>
<version>2.10.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.bcel</groupId>
<artifactId>bcel</artifactId>
<version>6.7.0</version>
<version>6.10.0</version>
<scope>test</scope>
</dependency>
@@ -814,7 +824,7 @@
<dependency>
<groupId>org.mock-server</groupId>
<artifactId>mockserver-junit-rule</artifactId>
<version>5.11.2</version>
<version>5.15.0</version>
<scope>test</scope>
<exclusions>
<!-- Exclude snakeyaml to avoid conflicts with: spring-boot-starter-cache -->
@@ -856,75 +866,4 @@
</exclusions>
</dependency>
</dependencies>
<dependencyManagement>
<dependencies>
<!-- for mockserver -->
<!-- Solve dependency convergence issues related to Solr and
'mockserver-junit-rule' by selecting the versions we want to use. -->
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-buffer</artifactId>
<version>4.1.106.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-transport</artifactId>
<version>4.1.106.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-transport-native-unix-common</artifactId>
<version>4.1.106.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-common</artifactId>
<version>4.1.106.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-handler</artifactId>
<version>4.1.106.Final</version>
</dependency>
<dependency>
<groupId>io.netty</groupId>
<artifactId>netty-codec</artifactId>
<version>4.1.106.Final</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>
<artifactId>velocity-engine-core</artifactId>
<version>2.3</version>
</dependency>
<dependency>
<groupId>org.xmlunit</groupId>
<artifactId>xmlunit-core</artifactId>
<version>2.10.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.github.java-json-tools</groupId>
<artifactId>json-schema-validator</artifactId>
<version>2.2.14</version>
</dependency>
<dependency>
<groupId>jakarta.validation</groupId>
<artifactId>jakarta.validation-api</artifactId>
<version>3.0.2</version>
</dependency>
<dependency>
<groupId>io.swagger</groupId>
<artifactId>swagger-core</artifactId>
<version>1.6.2</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.13.11</version>
<scope>test</scope>
</dependency>
</dependencies>
</dependencyManagement>
</project>

9
dspace-api/src/main/java/org/dspace/app/mediafilter/TikaTextExtractionFilter.java
View File

@@ -18,6 +18,7 @@ import java.nio.charset.StandardCharsets;
import org.apache.commons.lang.StringUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.poi.util.IOUtils;
import org.apache.tika.Tika;
import org.apache.tika.exception.TikaException;
import org.apache.tika.metadata.Metadata;
@@ -72,21 +73,23 @@ public class TikaTextExtractionFilter
// Not using temporary file. We'll use Tika's default in-memory parsing.
// Get maximum characters to extract. Default is 100,000 chars, which is also Tika's default setting.
String extractedText;
int maxChars = configurationService.getIntProperty("textextractor.max-chars", 100000);
int maxChars = configurationService.getIntProperty("textextractor.max-chars", 100_000);
try {
// Use Tika to extract text from input. Tika will automatically detect the file type.
Tika tika = new Tika();
tika.setMaxStringLength(maxChars); // Tell Tika the maximum number of characters to extract
IOUtils.setByteArrayMaxOverride(
configurationService.getIntProperty("textextractor.max-array", 100_000_000));
extractedText = tika.parseToString(source);
} catch (IOException e) {
System.err.format("Unable to extract text from bitstream in Item %s%n", currentItem.getID().toString());
e.printStackTrace();
e.printStackTrace(System.err);
log.error("Unable to extract text from bitstream in Item {}", currentItem.getID().toString(), e);
throw e;
} catch (OutOfMemoryError oe) {
System.err.format("OutOfMemoryError occurred when extracting text from bitstream in Item %s. " +
"You may wish to enable 'textextractor.use-temp-file'.%n", currentItem.getID().toString());
oe.printStackTrace();
oe.printStackTrace(System.err);
log.error("OutOfMemoryError occurred when extracting text from bitstream in Item {}. " +
"You may wish to enable 'textextractor.use-temp-file'.", currentItem.getID().toString(), oe);
throw oe;

13
dspace-api/src/main/java/org/dspace/app/statistics/LogAnalyser.java
View File

@@ -281,10 +281,14 @@ public class LogAnalyser {
*/
private static String fileTemplate = "dspace\\.log.*";
private static final ConfigurationService configurationService =
DSpaceServicesFactory.getInstance().getConfigurationService();
/**
* the configuration file from which to configure the analyser
*/
private static String configFile;
private static String configFile = configurationService.getProperty("dspace.dir")
+ File.separator + "config" + File.separator + "dstat.cfg";
/**
* the output file to which to write aggregation data
@@ -616,8 +620,6 @@ public class LogAnalyser {
}
// now do the host name and url lookup
ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
hostName = Utils.getHostName(configurationService.getProperty("dspace.ui.url"));
name = configurationService.getProperty("dspace.name").trim();
url = configurationService.getProperty("dspace.ui.url").trim();
@@ -658,8 +660,6 @@ public class LogAnalyser {
String myConfigFile, String myOutFile,
Date myStartDate, Date myEndDate,
boolean myLookUp) {
ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
if (myLogDir != null) {
logDir = myLogDir;
@@ -673,9 +673,6 @@ public class LogAnalyser {
if (myConfigFile != null) {
configFile = myConfigFile;
} else {
configFile = configurationService.getProperty("dspace.dir")
+ File.separator + "config" + File.separator + "dstat.cfg";
}
if (myStartDate != null) {

2
dspace-api/src/main/java/org/dspace/app/statistics/package.html
View File

@@ -46,8 +46,6 @@ Several "stock" implementations are provided.
<dd>writes event records to the Java logger.</dd>
<dt>{@link org.dspace.statistics.SolrLoggerUsageEventListener SolrLoggerUsageEventListener}</dt>
<dd>writes event records to Solr.</dd>
<dt>{@link org.dspace.google.GoogleRecorderEventListener GoogleRecorderEventListener}<.dt>
<dd>writes event records to Google Analytics.</dd>
</dl>
</body>
</html>

4
dspace-api/src/main/java/org/dspace/app/util/AuthorizeUtil.java
View File

@@ -523,9 +523,9 @@ public class AuthorizeUtil {
for (Collection coll : colls) {
if (!AuthorizeConfiguration
.canCollectionAdminPerformItemReinstatiate()) {
.canCollectionAdminPerformItemReinstate()) {
if (AuthorizeConfiguration
.canCommunityAdminPerformItemReinstatiate()
.canCommunityAdminPerformItemReinstate()
&& authorizeService.authorizeActionBoolean(context,
coll.getCommunities().get(0), Constants.ADMIN)) {
// authorized

4
dspace-api/src/main/java/org/dspace/app/util/DCInput.java
View File

@@ -163,7 +163,7 @@ public class DCInput {
* The scope of the input sets, this restricts hidden metadata fields from
* view by the end user during submission.
*/
public static final String SUBMISSION_SCOPE = "submit";
public static final String SUBMISSION_SCOPE = "submission";
/**
* Class constructor for creating a DCInput object based on the contents of
@@ -262,7 +262,7 @@ public class DCInput {
/**
* Is this DCInput for display in the given scope? The scope should be
* either "workflow" or "submit", as per the input forms definition. If the
* either "workflow" or "submission", as per the input forms definition. If the
* internal visibility is set to "null" then this will always return true.
*
* @param scope String identifying the scope that this input's visibility

24
dspace-api/src/main/java/org/dspace/app/util/OpenSearchServiceImpl.java
View File

@@ -14,7 +14,6 @@ import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import com.rometools.modules.opensearch.OpenSearchModule;
import com.rometools.modules.opensearch.entity.OSQuery;
@@ -58,12 +57,12 @@ public class OpenSearchServiceImpl implements OpenSearchService {
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(OpenSearchServiceImpl.class);
// Namespaces used
protected final String osNs = "http://a9.com/-/spec/opensearch/1.1/";
protected final static String osNs = "http://a9.com/-/spec/opensearch/1.1/";
@Autowired(required = true)
@Autowired
protected ConfigurationService configurationService;
@Autowired(required = true)
@Autowired
protected HandleService handleService;
protected OpenSearchServiceImpl() {
@@ -119,11 +118,10 @@ public class OpenSearchServiceImpl implements OpenSearchService {
@Override
public String getResultsString(Context context, String format, String query, int totalResults, int start,
int pageSize,
IndexableObject scope, List<IndexableObject> results,
Map<String, String> labels) throws IOException {
int pageSize, IndexableObject scope, List<IndexableObject> results)
throws IOException {
try {
return getResults(context, format, query, totalResults, start, pageSize, scope, results, labels)
return getResults(context, format, query, totalResults, start, pageSize, scope, results)
.outputString();
} catch (FeedException e) {
log.error(e.toString(), e);
@@ -133,11 +131,10 @@ public class OpenSearchServiceImpl implements OpenSearchService {
@Override
public Document getResultsDoc(Context context, String format, String query, int totalResults, int start,
int pageSize,
IndexableObject scope, List<IndexableObject> results, Map<String, String> labels)
int pageSize, IndexableObject scope, List<IndexableObject> results)
throws IOException {
try {
return getResults(context, format, query, totalResults, start, pageSize, scope, results, labels)
return getResults(context, format, query, totalResults, start, pageSize, scope, results)
.outputW3CDom();
} catch (FeedException e) {
log.error(e.toString(), e);
@@ -146,8 +143,7 @@ public class OpenSearchServiceImpl implements OpenSearchService {
}
protected SyndicationFeed getResults(Context context, String format, String query, int totalResults, int start,
int pageSize, IndexableObject scope,
List<IndexableObject> results, Map<String, String> labels) {
int pageSize, IndexableObject scope, List<IndexableObject> results) {
// Encode results in requested format
if ("rss".equals(format)) {
format = "rss_2.0";
@@ -156,7 +152,7 @@ public class OpenSearchServiceImpl implements OpenSearchService {
}
SyndicationFeed feed = new SyndicationFeed();
feed.populate(null, context, scope, results, labels);
feed.populate(null, context, scope, results);
feed.setType(format);
feed.addModule(openSearchMarkup(query, totalResults, start, pageSize));
return feed;

38
dspace-api/src/main/java/org/dspace/app/util/SyndicationFeed.java
View File

@@ -11,6 +11,7 @@ import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -135,8 +136,6 @@ public class SyndicationFeed {
protected String[] podcastableMIMETypes =
configurationService.getArrayProperty("webui.feed.podcast.mimetypes", new String[] {"audio/x-mpeg"});
// -------- Instance variables:
// the feed object we are building
protected SyndFeed feed = null;
@@ -146,9 +145,6 @@ public class SyndicationFeed {
protected CommunityService communityService;
protected ItemService itemService;
/**
* Constructor.
*/
public SyndicationFeed() {
feed = new SyndFeedImpl();
ContentServiceFactory contentServiceFactory = ContentServiceFactory.getInstance();
@@ -157,16 +153,6 @@ public class SyndicationFeed {
communityService = contentServiceFactory.getCommunityService();
}
/**
* Returns list of metadata selectors used to compose the description element
*
* @return selector list - format 'schema.element[.qualifier]'
*/
public static String[] getDescriptionSelectors() {
return (String[]) ArrayUtils.clone(descriptionFields);
}
/**
* Fills in the feed and entry-level metadata from DSpace objects.
*
@@ -174,15 +160,17 @@ public class SyndicationFeed {
* @param context context
* @param dso the scope
* @param items array of objects
* @param labels label map
*/
public void populate(HttpServletRequest request, Context context, IndexableObject dso,
List<IndexableObject> items, Map<String, String> labels) {
List<IndexableObject> items) {
String logoURL = null;
String objectURL = null;
String defaultTitle = null;
boolean podcastFeed = false;
this.request = request;
Map<String, String> labels = getLabels();
// dso is null for the whole site, or a search without scope
if (dso == null) {
defaultTitle = configurationService.getProperty("dspace.name");
@@ -553,5 +541,19 @@ public class SyndicationFeed {
List<MetadataValue> dcv = itemService.getMetadataByMetadataString(item, field);
return (dcv.size() > 0) ? dcv.get(0).getValue() : null;
}
}
/**
* Internal method to get labels for the returned document
*/
private Map<String, String> getLabels() {
// TODO: get strings from translation file or configuration
Map<String, String> labelMap = new HashMap<>();
labelMap.put(SyndicationFeed.MSG_UNTITLED, "notitle");
labelMap.put(SyndicationFeed.MSG_LOGO_TITLE, "logo.title");
labelMap.put(SyndicationFeed.MSG_FEED_DESCRIPTION, "general-feed.description");
for (String selector : descriptionFields) {
labelMap.put("metadata." + selector, selector);
}
return labelMap;
}
}

11
dspace-api/src/main/java/org/dspace/app/util/service/OpenSearchService.java
View File

@@ -10,7 +10,6 @@ package org.dspace.app.util.service;
import java.io.IOException;
import java.sql.SQLException;
import java.util.List;
import java.util.Map;
import org.dspace.content.DSpaceObject;
import org.dspace.core.Context;
@@ -86,14 +85,12 @@ public interface OpenSearchService {
* @param pageSize - page size
* @param scope - search scope, null or the community/collection
* @param results the retrieved DSpace objects satisfying search
* @param labels labels to apply - format specific
* @return formatted search results
* @throws IOException if IO error
*/
public String getResultsString(Context context, String format, String query, int totalResults, int start,
int pageSize,
IndexableObject scope, List<IndexableObject> results,
Map<String, String> labels) throws IOException;
int pageSize, IndexableObject scope, List<IndexableObject> results)
throws IOException;
/**
* Returns a formatted set of search results as a document
@@ -106,13 +103,11 @@ public interface OpenSearchService {
* @param pageSize - page size
* @param scope - search scope, null or the community/collection
* @param results the retrieved DSpace objects satisfying search
* @param labels labels to apply - format specific
* @return formatted search results
* @throws IOException if IO error
*/
public Document getResultsDoc(Context context, String format, String query, int totalResults, int start,
int pageSize,
IndexableObject scope, List<IndexableObject> results, Map<String, String> labels)
int pageSize, IndexableObject scope, List<IndexableObject> results)
throws IOException;
public DSpaceObject resolveScope(Context context, String scope) throws SQLException;

80
dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java
View File

@@ -17,6 +17,7 @@ import java.util.Collections;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import javax.naming.NamingEnumeration;
import javax.naming.NamingException;
import javax.naming.directory.Attribute;
@@ -68,12 +69,8 @@ import org.dspace.services.factory.DSpaceServicesFactory;
* @author Ivan Masár
* @author Michael Plate
*/
public class LDAPAuthentication
implements AuthenticationMethod {
public class LDAPAuthentication implements AuthenticationMethod {
/**
* log4j category
*/
private static final Logger log
= org.apache.logging.log4j.LogManager.getLogger(LDAPAuthentication.class);
@@ -130,7 +127,7 @@ public class LDAPAuthentication
return false;
}
/*
/**
* This is an explicit method.
*/
@Override
@@ -138,7 +135,7 @@ public class LDAPAuthentication
return false;
}
/*
/**
* Add authenticated users to the group defined in dspace.cfg by
* the login.specialgroup key.
*/
@@ -177,7 +174,7 @@ public class LDAPAuthentication
return Collections.EMPTY_LIST;
}
/*
/**
* Authenticate the given credentials.
* This is the heart of the authentication method: test the
* credentials for authenticity, and if accepted, attempt to match
@@ -187,7 +184,7 @@ public class LDAPAuthentication
* @param context
* DSpace context, will be modified (ePerson set) upon success.
*
* @param username
* @param netid
* Username (or email address) when method is explicit. Use null for
* implicit method.
*
@@ -250,7 +247,7 @@ public class LDAPAuthentication
}
// Check a DN was found
if ((dn == null) || (dn.trim().equals(""))) {
if (StringUtils.isBlank(dn)) {
log.info(LogHelper
.getHeader(context, "failed_login", "no DN found for user " + netid));
return BAD_CREDENTIALS;
@@ -269,6 +266,18 @@ public class LDAPAuthentication
context.setCurrentUser(eperson);
request.setAttribute(LDAP_AUTHENTICATED, true);
// update eperson's attributes
context.turnOffAuthorisationSystem();
setEpersonAttributes(context, eperson, ldap, Optional.empty());
try {
ePersonService.update(context, eperson);
context.dispatchEvents();
} catch (AuthorizeException e) {
log.warn("update of eperson " + eperson.getID() + " failed", e);
} finally {
context.restoreAuthSystemState();
}
// assign user to groups based on ldap dn
assignGroups(dn, ldap.ldapGroup, context);
@@ -313,14 +322,13 @@ public class LDAPAuthentication
log.info(LogHelper.getHeader(context,
"type=ldap-login", "type=ldap_but_already_email"));
context.turnOffAuthorisationSystem();
eperson.setNetid(netid.toLowerCase());
setEpersonAttributes(context, eperson, ldap, Optional.of(netid));
ePersonService.update(context, eperson);
context.dispatchEvents();
context.restoreAuthSystemState();
context.setCurrentUser(eperson);
request.setAttribute(LDAP_AUTHENTICATED, true);
// assign user to groups based on ldap dn
assignGroups(dn, ldap.ldapGroup, context);
@@ -331,20 +339,7 @@ public class LDAPAuthentication
try {
context.turnOffAuthorisationSystem();
eperson = ePersonService.create(context);
if (StringUtils.isNotEmpty(email)) {
eperson.setEmail(email);
}
if (StringUtils.isNotEmpty(ldap.ldapGivenName)) {
eperson.setFirstName(context, ldap.ldapGivenName);
}
if (StringUtils.isNotEmpty(ldap.ldapSurname)) {
eperson.setLastName(context, ldap.ldapSurname);
}
if (StringUtils.isNotEmpty(ldap.ldapPhone)) {
ePersonService.setMetadataSingleValue(context, eperson,
MD_PHONE, ldap.ldapPhone, null);
}
eperson.setNetid(netid.toLowerCase());
setEpersonAttributes(context, eperson, ldap, Optional.of(netid));
eperson.setCanLogIn(true);
authenticationService.initEPerson(context, request, eperson);
ePersonService.update(context, eperson);
@@ -382,6 +377,29 @@ public class LDAPAuthentication
return BAD_ARGS;
}
/**
* Update eperson's attributes
*/
private void setEpersonAttributes(Context context, EPerson eperson, SpeakerToLDAP ldap, Optional<String> netid)
throws SQLException {
if (StringUtils.isNotEmpty(ldap.ldapEmail)) {
eperson.setEmail(ldap.ldapEmail);
}
if (StringUtils.isNotEmpty(ldap.ldapGivenName)) {
eperson.setFirstName(context, ldap.ldapGivenName);
}
if (StringUtils.isNotEmpty(ldap.ldapSurname)) {
eperson.setLastName(context, ldap.ldapSurname);
}
if (StringUtils.isNotEmpty(ldap.ldapPhone)) {
ePersonService.setMetadataSingleValue(context, eperson, MD_PHONE, ldap.ldapPhone, null);
}
if (netid.isPresent()) {
eperson.setNetid(netid.get().toLowerCase());
}
}
/**
* Internal class to manage LDAP query and results, mainly
* because there are multiple values to return.
@@ -503,6 +521,7 @@ public class LDAPAuthentication
} else {
searchName = ldap_provider_url + ldap_search_context;
}
@SuppressWarnings("BanJNDI")
NamingEnumeration<SearchResult> answer = ctx.search(
searchName,
"(&({0}={1}))", new Object[] {ldap_id_field,
@@ -553,7 +572,7 @@ public class LDAPAuthentication
att = atts.get(attlist[4]);
if (att != null) {
// loop through all groups returned by LDAP
ldapGroup = new ArrayList<String>();
ldapGroup = new ArrayList<>();
for (NamingEnumeration val = att.getAll(); val.hasMoreElements(); ) {
ldapGroup.add((String) val.next());
}
@@ -633,7 +652,8 @@ public class LDAPAuthentication
ctx.addToEnvironment(javax.naming.Context.AUTHORITATIVE, "true");
ctx.addToEnvironment(javax.naming.Context.REFERRAL, "follow");
// dummy operation to check if authentication has succeeded
ctx.getAttributes("");
@SuppressWarnings("BanJNDI")
Attributes trash = ctx.getAttributes("");
} else if (!useTLS) {
// Authenticate
env.put(javax.naming.Context.SECURITY_AUTHENTICATION, "Simple");
@@ -671,7 +691,7 @@ public class LDAPAuthentication
}
}
/*
/**
* Returns the URL of an external login page which is not applicable for this authn method.
*
* Note: Prior to DSpace 7, this method return the page of login servlet.
@@ -699,7 +719,7 @@ public class LDAPAuthentication
return "ldap";
}
/*
/**
* Add authenticated users to the group defined in dspace.cfg by
* the authentication-ldap.login.groupmap.* key.
*

8
dspace-api/src/main/java/org/dspace/authorize/AuthorizeConfiguration.java
View File

@@ -174,9 +174,9 @@ public class AuthorizeConfiguration {
*
* @return true/false
*/
public static boolean canCommunityAdminPerformItemReinstatiate() {
public static boolean canCommunityAdminPerformItemReinstate() {
init();
return configurationService.getBooleanProperty("core.authorization.community-admin.item.reinstatiate", true);
return configurationService.getBooleanProperty("core.authorization.community-admin.item.reinstate", true);
}
/**
@@ -306,9 +306,9 @@ public class AuthorizeConfiguration {
*
* @return true/false
*/
public static boolean canCollectionAdminPerformItemReinstatiate() {
public static boolean canCollectionAdminPerformItemReinstate() {
init();
return configurationService.getBooleanProperty("core.authorization.collection-admin.item.reinstatiate", true);
return configurationService.getBooleanProperty("core.authorization.collection-admin.item.reinstate", true);
}
/**

30
dspace-api/src/main/java/org/dspace/browse/BrowseEngine.java
View File

@@ -422,9 +422,6 @@ public class BrowseEngine {
}
}
// this is the total number of results in answer to the query
int total = getTotalResults(true);
// set the ordering field (there is only one option)
dao.setOrderField("sort_value");
@@ -444,6 +441,9 @@ public class BrowseEngine {
dao.setOffset(offset);
dao.setLimit(scope.getResultsPerPage());
// this is the total number of results in answer to the query
int total = getTotalResults(true);
// Holder for the results
List<String[]> results = null;
@@ -680,33 +680,9 @@ public class BrowseEngine {
// tell the browse query whether we are distinct
dao.setDistinct(distinct);
// ensure that the select is set to "*"
String[] select = {"*"};
dao.setCountValues(select);
// FIXME: it would be nice to have a good way of doing this in the DAO
// now reset all of the fields that we don't want to have constraining
// our count, storing them locally to reinstate later
String focusField = dao.getJumpToField();
String focusValue = dao.getJumpToValue();
int limit = dao.getLimit();
int offset = dao.getOffset();
dao.setJumpToField(null);
dao.setJumpToValue(null);
dao.setLimit(-1);
dao.setOffset(-1);
// perform the query and get the result
int count = dao.doCountQuery();
// now put back the values we removed for this method
dao.setJumpToField(focusField);
dao.setJumpToValue(focusValue);
dao.setLimit(limit);
dao.setOffset(offset);
dao.setCountValues(null);
log.debug(LogHelper.getHeader(context, "get_total_results_return", "return=" + count));
return count;

42
dspace-api/src/main/java/org/dspace/browse/BrowseIndex.java
View File

@@ -543,19 +543,6 @@ public class BrowseIndex {
return getTableName(false, false, true, false);
}
/**
* Get the name of the column that is used to store the default value column
*
* @return the name of the value column
*/
public String getValueColumn() {
if (!isDate()) {
return "sort_text_value";
} else {
return "text_value";
}
}
/**
* Get the name of the primary key index column
*
@@ -565,35 +552,6 @@ public class BrowseIndex {
return "id";
}
/**
* Is this browse index type for a title?
*
* @return true if title type, false if not
*/
// public boolean isTitle()
// {
// return "title".equals(getDataType());
// }
/**
* Is the browse index type for a date?
*
* @return true if date type, false if not
*/
public boolean isDate() {
return "date".equals(getDataType());
}
/**
* Is the browse index type for a plain text type?
*
* @return true if plain text type, false if not
*/
// public boolean isText()
// {
// return "text".equals(getDataType());
// }
/**
* Is the browse index of display type single?
*

32
dspace-api/src/main/java/org/dspace/browse/SolrBrowseDAO.java
View File

@@ -13,6 +13,8 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import com.fasterxml.jackson.databind.node.JsonNodeFactory;
import com.fasterxml.jackson.databind.node.ObjectNode;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.apache.solr.client.solrj.util.ClientUtils;
@@ -180,18 +182,33 @@ public class SolrBrowseDAO implements BrowseDAO {
addDefaultFilterQueries(query);
if (distinct) {
DiscoverFacetField dff;
// To get the number of distinct values we use the next "json.facet" query param
// {"entries_count": {"type":"terms","field": "<fieldName>_filter", "limit":0, "numBuckets":true}}"
ObjectNode jsonFacet = JsonNodeFactory.instance.objectNode();
ObjectNode entriesCount = JsonNodeFactory.instance.objectNode();
entriesCount.put("type", "terms");
entriesCount.put("field", facetField + "_filter");
entriesCount.put("limit", 0);
entriesCount.put("numBuckets", true);
jsonFacet.set("entries_count", entriesCount);
if (StringUtils.isNotBlank(startsWith)) {
dff = new DiscoverFacetField(facetField,
DiscoveryConfigurationParameters.TYPE_TEXT, -1,
DiscoveryConfigurationParameters.SORT.VALUE, startsWith);
DiscoveryConfigurationParameters.TYPE_TEXT, limit,
DiscoveryConfigurationParameters.SORT.VALUE, startsWith, offset);
// Add the prefix to the json facet query
entriesCount.put("prefix", startsWith);
} else {
dff = new DiscoverFacetField(facetField,
DiscoveryConfigurationParameters.TYPE_TEXT, -1,
DiscoveryConfigurationParameters.SORT.VALUE);
DiscoveryConfigurationParameters.TYPE_TEXT, limit,
DiscoveryConfigurationParameters.SORT.VALUE, offset);
}
query.addFacetField(dff);
query.setFacetMinCount(1);
query.setMaxResults(0);
query.addProperty("json.facet", jsonFacet.toString());
} else {
query.setMaxResults(limit/* > 0 ? limit : 20*/);
if (offset > 0) {
@@ -248,8 +265,7 @@ public class SolrBrowseDAO implements BrowseDAO {
DiscoverResult resp = getSolrResponse();
int count = 0;
if (distinct) {
List<FacetResult> facetResults = resp.getFacetResult(facetField);
count = facetResults.size();
count = (int) resp.getTotalEntries();
} else {
// we need to cast to int to respect the BrowseDAO contract...
count = (int) resp.getTotalSearchResults();
@@ -266,8 +282,8 @@ public class SolrBrowseDAO implements BrowseDAO {
DiscoverResult resp = getSolrResponse();
List<FacetResult> facet = resp.getFacetResult(facetField);
int count = doCountQuery();
int start = offset > 0 ? offset : 0;
int max = limit > 0 ? limit : count; //if negative, return everything
int start = 0;
int max = facet.size();
List<String[]> result = new ArrayList<>();
if (ascending) {
for (int i = start; i < (start + max) && i < count; i++) {

2
dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java
View File

@@ -67,6 +67,7 @@ import org.dspace.event.Event;
import org.dspace.harvest.HarvestedItem;
import org.dspace.harvest.service.HarvestedItemService;
import org.dspace.identifier.DOI;
import org.dspace.identifier.DOIIdentifierProvider;
import org.dspace.identifier.IdentifierException;
import org.dspace.identifier.service.DOIService;
import org.dspace.identifier.service.IdentifierService;
@@ -851,6 +852,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
DOI doi = doiService.findDOIByDSpaceObject(context, item);
if (doi != null) {
doi.setDSpaceObject(null);
doi.setStatus(DOIIdentifierProvider.TO_BE_DELETED);
}
// remove version attached to the item

8
dspace-api/src/main/java/org/dspace/content/WorkspaceItemServiceImpl.java
View File

@@ -178,6 +178,14 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
@Override
public WorkspaceItem create(Context c, WorkflowItem workflowItem) throws SQLException, AuthorizeException {
WorkspaceItem potentialDuplicate = findByItem(c, workflowItem.getItem());
if (potentialDuplicate != null) {
throw new IllegalArgumentException(String.format(
"A workspace item referring to item %s already exists (%d)",
workflowItem.getItem().getID(),
potentialDuplicate.getID()
));
}
WorkspaceItem workspaceItem = workspaceItemDAO.create(c, new WorkspaceItem());
workspaceItem.setItem(workflowItem.getItem());
workspaceItem.setCollection(workflowItem.getCollection());

64
dspace-api/src/main/java/org/dspace/content/authority/DSpaceControlledVocabulary.java
View File

@@ -8,6 +8,7 @@
package org.dspace.content.authority;
import java.io.File;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
@@ -65,14 +66,17 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
protected static String labelTemplate = "//node[@label = '%s']";
protected static String idParentTemplate = "//node[@id = '%s']/parent::isComposedBy/parent::node";
protected static String rootTemplate = "/node";
protected static String idAttribute = "id";
protected static String labelAttribute = "label";
protected static String pluginNames[] = null;
protected String vocabularyName = null;
protected InputSource vocabulary = null;
protected Boolean suggestHierarchy = false;
protected Boolean storeHierarchy = true;
protected String hierarchyDelimiter = "::";
protected Integer preloadLevel = 1;
protected String valueAttribute = labelAttribute;
protected String valueTemplate = labelTemplate;
public DSpaceControlledVocabulary() {
super();
@@ -115,7 +119,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
}
}
protected void init() {
protected void init(String locale) {
if (vocabulary == null) {
ConfigurationService config = DSpaceServicesFactory.getInstance().getConfigurationService();
@@ -125,13 +129,25 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
File.separator + "controlled-vocabularies" + File.separator;
String configurationPrefix = "vocabulary.plugin." + vocabularyName;
storeHierarchy = config.getBooleanProperty(configurationPrefix + ".hierarchy.store", storeHierarchy);
boolean storeIDs = config.getBooleanProperty(configurationPrefix + ".storeIDs", false);
suggestHierarchy = config.getBooleanProperty(configurationPrefix + ".hierarchy.suggest", suggestHierarchy);
preloadLevel = config.getIntProperty(configurationPrefix + ".hierarchy.preloadLevel", preloadLevel);
String configuredDelimiter = config.getProperty(configurationPrefix + ".delimiter");
if (configuredDelimiter != null) {
hierarchyDelimiter = configuredDelimiter.replaceAll("(^\"|\"$)", "");
}
if (storeIDs) {
valueAttribute = idAttribute;
valueTemplate = idTemplate;
}
String filename = vocabulariesPath + vocabularyName + ".xml";
if (StringUtils.isNotEmpty(locale)) {
String localizedFilename = vocabulariesPath + vocabularyName + "_" + locale + ".xml";
if (Paths.get(localizedFilename).toFile().exists()) {
filename = localizedFilename;
}
}
log.info("Loading " + filename);
vocabulary = new InputSource(filename);
}
@@ -144,9 +160,9 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
return ("");
} else {
String parentValue = buildString(node.getParentNode());
Node currentLabel = node.getAttributes().getNamedItem("label");
if (currentLabel != null) {
String currentValue = currentLabel.getNodeValue();
Node currentNodeValue = node.getAttributes().getNamedItem(valueAttribute);
if (currentNodeValue != null) {
String currentValue = currentNodeValue.getNodeValue();
if (parentValue.equals("")) {
return currentValue;
} else {
@@ -160,12 +176,13 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
@Override
public Choices getMatches(String text, int start, int limit, String locale) {
init();
init(locale);
log.debug("Getting matches for '" + text + "'");
String xpathExpression = "";
String[] textHierarchy = text.split(hierarchyDelimiter, -1);
for (int i = 0; i < textHierarchy.length; i++) {
xpathExpression += String.format(xpathTemplate, textHierarchy[i].replaceAll("'", "&apos;").toLowerCase());
xpathExpression +=
String.format(xpathTemplate, textHierarchy[i].replaceAll("'", "&apos;").toLowerCase());
}
XPath xpath = XPathFactory.newInstance().newXPath();
int total = 0;
@@ -184,12 +201,13 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
@Override
public Choices getBestMatch(String text, String locale) {
init();
init(locale);
log.debug("Getting best matches for '" + text + "'");
String xpathExpression = "";
String[] textHierarchy = text.split(hierarchyDelimiter, -1);
for (int i = 0; i < textHierarchy.length; i++) {
xpathExpression += String.format(labelTemplate, textHierarchy[i].replaceAll("'", "&apos;"));
xpathExpression +=
String.format(valueTemplate, textHierarchy[i].replaceAll("'", "&apos;"));
}
XPath xpath = XPathFactory.newInstance().newXPath();
List<Choice> choices = new ArrayList<Choice>();
@@ -205,19 +223,19 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
@Override
public String getLabel(String key, String locale) {
return getNodeLabel(key, this.suggestHierarchy);
return getNodeValue(key, locale, this.suggestHierarchy);
}
@Override
public String getValue(String key, String locale) {
return getNodeLabel(key, this.storeHierarchy);
return getNodeValue(key, locale, this.storeHierarchy);
}
@Override
public Choice getChoice(String authKey, String locale) {
Node node;
try {
node = getNode(authKey);
node = getNode(authKey, locale);
} catch (XPathExpressionException e) {
return null;
}
@@ -226,27 +244,27 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
@Override
public boolean isHierarchical() {
init();
init(null);
return true;
}
@Override
public Choices getTopChoices(String authorityName, int start, int limit, String locale) {
init();
init(locale);
String xpathExpression = rootTemplate;
return getChoicesByXpath(xpathExpression, start, limit);
}
@Override
public Choices getChoicesByParent(String authorityName, String parentId, int start, int limit, String locale) {
init();
init(locale);
String xpathExpression = String.format(idTemplate, parentId);
return getChoicesByXpath(xpathExpression, start, limit);
}
@Override
public Choice getParentChoice(String authorityName, String childId, String locale) {
init();
init(locale);
try {
String xpathExpression = String.format(idParentTemplate, childId);
Choice choice = createChoiceFromNode(getNodeFromXPath(xpathExpression));
@@ -259,7 +277,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
@Override
public Integer getPreloadLevel() {
init();
init(null);
return preloadLevel;
}
@@ -270,8 +288,8 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
return false;
}
private Node getNode(String key) throws XPathExpressionException {
init();
private Node getNode(String key, String locale) throws XPathExpressionException {
init(locale);
String xpathExpression = String.format(idTemplate, key);
Node node = getNodeFromXPath(xpathExpression);
return node;
@@ -319,16 +337,16 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
return extras;
}
private String getNodeLabel(String key, boolean useHierarchy) {
private String getNodeValue(String key, String locale, boolean useHierarchy) {
try {
Node node = getNode(key);
Node node = getNode(key, locale);
if (Objects.isNull(node)) {
return null;
}
if (useHierarchy) {
return this.buildString(node);
} else {
return node.getAttributes().getNamedItem("label").getNodeValue();
return node.getAttributes().getNamedItem(valueAttribute).getNodeValue();
}
} catch (XPathExpressionException e) {
return ("");
@@ -349,7 +367,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
if (this.storeHierarchy) {
return hierarchy;
} else {
return node.getAttributes().getNamedItem("label").getNodeValue();
return node.getAttributes().getNamedItem(valueAttribute).getNodeValue();
}
}

2
dspace-api/src/main/java/org/dspace/core/AbstractHibernateDAO.java
View File

@@ -313,7 +313,7 @@ public abstract class AbstractHibernateDAO<T> implements GenericDAO<T> {
org.hibernate.query.Query hquery = query.unwrap(org.hibernate.query.Query.class);
Stream<T> stream = hquery.stream();
Iterator<T> iter = stream.iterator();
return new AbstractIterator<T> () {
return new AbstractIterator<T>() {
@Override
protected T computeNext() {
return iter.hasNext() ? iter.next() : endOfData();

14
dspace-api/src/main/java/org/dspace/core/Context.java
View File

@@ -883,7 +883,19 @@ public class Context implements AutoCloseable {
}
/**
* Remove an entity from the cache. This is necessary when batch processing a large number of items.
* Remove all entities from the cache and reload the current user entity. This is useful when batch processing
* a large number of entities when the calling code requires the cache to be completely cleared before continuing.
*
* @throws SQLException if a database error occurs.
*/
public void uncacheEntities() throws SQLException {
dbConnection.uncacheEntities();
reloadContextBoundEntities();
}
/**
* Remove an entity from the cache. This is useful when batch processing a large number of entities
* when the calling code needs to retain some items in the cache while removing others.
*
* @param entity The entity to reload
* @param <E> The class of the entity. The entity must implement the {@link ReloadableEntity} interface.

32
dspace-api/src/main/java/org/dspace/core/DBConnection.java
View File

@@ -124,28 +124,38 @@ public interface DBConnection<T> {
public long getCacheSize() throws SQLException;
/**
* Reload a DSpace object from the database. This will make sure the object
* Reload an entity from the database. This will make sure the object
* is valid and stored in the cache. The returned object should be used
* henceforth instead of the passed object.
*
* @param <E> type of {@link entity}
* @param entity The DSpace object to reload
* @param <E> type of entity.
* @param entity The entity to reload.
* @return the reloaded entity.
* @throws java.sql.SQLException passed through.
* @throws SQLException passed through.
*/
public <E extends ReloadableEntity> E reloadEntity(E entity) throws SQLException;
/**
* Remove a DSpace object from the session cache when batch processing a
* large number of objects.
* Remove all entities from the session cache.
*
* <p>Objects removed from cache are not saved in any way. Therefore, if you
* have modified an object, you should be sure to {@link commit()} changes
* <p>Entities removed from cache are not saved in any way. Therefore, if you
* have modified any entities, you should be sure to {@link #commit()} changes
* before calling this method.
*
* @param <E> Type of {@link entity}
* @param entity The DSpace object to decache.
* @throws java.sql.SQLException passed through.
* @throws SQLException passed through.
*/
public void uncacheEntities() throws SQLException;
/**
* Remove an entity from the session cache.
*
* <p>Entities removed from cache are not saved in any way. Therefore, if you
* have modified the entity, you should be sure to {@link #commit()} changes
* before calling this method.
*
* @param <E> Type of entity.
* @param entity The entity to decache.
* @throws SQLException passed through.
*/
public <E extends ReloadableEntity> void uncacheEntity(E entity) throws SQLException;

5
dspace-api/src/main/java/org/dspace/core/HibernateDBConnection.java
View File

@@ -242,6 +242,11 @@ public class HibernateDBConnection implements DBConnection<Session> {
}
}
@Override
public void uncacheEntities() throws SQLException {
getSession().clear();
}
/**
* Evict an entity from the hibernate cache.
* <P>

26
dspace-api/src/main/java/org/dspace/ctask/general/BasicLinkChecker.java
View File

@@ -19,6 +19,8 @@ import org.dspace.content.Item;
import org.dspace.content.MetadataValue;
import org.dspace.curate.AbstractCurationTask;
import org.dspace.curate.Curator;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
/**
* A basic link checker that is designed to be extended. By default this link checker
@@ -42,6 +44,9 @@ public class BasicLinkChecker extends AbstractCurationTask {
// The log4j logger for this class
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(BasicLinkChecker.class);
protected static final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
/**
* Perform the link checking.
@@ -110,7 +115,8 @@ public class BasicLinkChecker extends AbstractCurationTask {
*/
protected boolean checkURL(String url, StringBuilder results) {
// Link check the URL
int httpStatus = getResponseStatus(url);
int redirects = 0;
int httpStatus = getResponseStatus(url, redirects);
if ((httpStatus >= 200) && (httpStatus < 300)) {
results.append(" - " + url + " = " + httpStatus + " - OK\n");
@@ -128,14 +134,24 @@ public class BasicLinkChecker extends AbstractCurationTask {
* @param url The url to open
* @return The HTTP response code (e.g. 200 / 301 / 404 / 500)
*/
protected int getResponseStatus(String url) {
protected int getResponseStatus(String url, int redirects) {
try {
URL theURL = new URL(url);
HttpURLConnection connection = (HttpURLConnection) theURL.openConnection();
int code = connection.getResponseCode();
connection.disconnect();
connection.setInstanceFollowRedirects(true);
int statusCode = connection.getResponseCode();
int maxRedirect = configurationService.getIntProperty("curate.checklinks.max-redirect", 0);
if ((statusCode == HttpURLConnection.HTTP_MOVED_TEMP || statusCode == HttpURLConnection.HTTP_MOVED_PERM ||
statusCode == HttpURLConnection.HTTP_SEE_OTHER)) {
connection.disconnect();
String newUrl = connection.getHeaderField("Location");
if (newUrl != null && (maxRedirect >= redirects || maxRedirect == -1)) {
redirects++;
return getResponseStatus(newUrl, redirects);
}
return code;
}
return statusCode;
} catch (IOException ioe) {
// Must be a bad URL

28
dspace-api/src/main/java/org/dspace/ctask/general/CreateMissingIdentifiers.java
View File

@@ -10,6 +10,7 @@ package org.dspace.ctask.general;
import java.io.IOException;
import java.sql.SQLException;
import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -25,7 +26,6 @@ import org.dspace.identifier.IdentifierProvider;
import org.dspace.identifier.VersionedHandleIdentifierProviderWithCanonicalHandles;
import org.dspace.identifier.factory.IdentifierServiceFactory;
import org.dspace.identifier.service.IdentifierService;
import org.dspace.services.factory.DSpaceServicesFactory;
/**
* Ensure that an object has all of the identifiers that it should, minting them
@@ -45,20 +45,6 @@ public class CreateMissingIdentifiers
return Curator.CURATE_SKIP;
}
// XXX Temporary escape when an incompatible provider is configured.
// XXX Remove this when the provider is fixed.
boolean compatible = DSpaceServicesFactory
.getInstance()
.getServiceManager()
.getServiceByName(
VersionedHandleIdentifierProviderWithCanonicalHandles.class.getCanonicalName(),
IdentifierProvider.class) == null;
if (!compatible) {
setResult("This task is not compatible with VersionedHandleIdentifierProviderWithCanonicalHandles");
return Curator.CURATE_ERROR;
}
// XXX End of escape
String typeText = Constants.typeText[dso.getType()];
// Get a Context
@@ -75,6 +61,18 @@ public class CreateMissingIdentifiers
.getInstance()
.getIdentifierService();
// XXX Temporary escape when an incompatible provider is configured.
// XXX Remove this when the provider is fixed.
List<IdentifierProvider> providerList = identifierService.getProviders();
boolean compatible =
providerList.stream().noneMatch(p -> p instanceof VersionedHandleIdentifierProviderWithCanonicalHandles);
if (!compatible) {
setResult("This task is not compatible with VersionedHandleIdentifierProviderWithCanonicalHandles");
return Curator.CURATE_ERROR;
}
// XXX End of escape
// Register any missing identifiers.
try {
identifierService.register(context, dso);

18
dspace-api/src/main/java/org/dspace/curate/Curation.java
View File

@@ -165,7 +165,7 @@ public class Curation extends DSpaceRunnable<CurationScriptConfiguration> {
* End of curation script; logs script time if -v verbose is set
*
* @param timeRun Time script was started
* @throws SQLException If DSpace contextx can't complete
* @throws SQLException If DSpace context can't complete
*/
private void endScript(long timeRun) throws SQLException {
context.complete();
@@ -185,7 +185,7 @@ public class Curation extends DSpaceRunnable<CurationScriptConfiguration> {
Curator curator = new Curator(handler);
OutputStream reporterStream;
if (null == this.reporter) {
reporterStream = new NullOutputStream();
reporterStream = NullOutputStream.NULL_OUTPUT_STREAM;
} else if ("-".equals(this.reporter)) {
reporterStream = System.out;
} else {
@@ -300,9 +300,17 @@ public class Curation extends DSpaceRunnable<CurationScriptConfiguration> {
// scope
if (this.commandLine.getOptionValue('s') != null) {
this.scope = this.commandLine.getOptionValue('s');
if (this.scope != null && Curator.TxScope.valueOf(this.scope.toUpperCase()) == null) {
this.handler.logError("Bad transaction scope '" + this.scope + "': only 'object', 'curation' or " +
"'open' recognized");
boolean knownScope;
try {
Curator.TxScope.valueOf(this.scope.toUpperCase());
knownScope = true;
} catch (IllegalArgumentException | NullPointerException e) {
knownScope = false;
}
if (!knownScope) {
this.handler.logError("Bad transaction scope '"
+ this.scope
+ "': only 'object', 'curation' or 'open' recognized");
throw new IllegalArgumentException(
"Bad transaction scope '" + this.scope + "': only 'object', 'curation' or " +
"'open' recognized");

11
dspace-api/src/main/java/org/dspace/discovery/DiscoverResult.java
View File

@@ -32,6 +32,9 @@ public class DiscoverResult {
private List<IndexableObject> indexableObjects;
private Map<String, List<FacetResult>> facetResults;
// Total count of facet entries calculated for a metadata browsing query
private long totalEntries;
/**
* A map that contains all the documents sougth after, the key is a string representation of the Indexable Object
*/
@@ -64,6 +67,14 @@ public class DiscoverResult {
this.totalSearchResults = totalSearchResults;
}
public long getTotalEntries() {
return totalEntries;
}
public void setTotalEntries(long totalEntries) {
this.totalEntries = totalEntries;
}
public int getStart() {
return start;
}

36
dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java
View File

@@ -1055,6 +1055,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
}
//Resolve our facet field values
resolveFacetFields(context, query, result, skipLoadingResponse, solrQueryResponse);
//Add total entries count for metadata browsing
resolveEntriesCount(result, solrQueryResponse);
}
// If any stale entries are found in the current page of results,
// we remove those stale entries and rerun the same query again.
@@ -1080,7 +1082,39 @@ public class SolrServiceImpl implements SearchService, IndexingService {
return result;
}
/**
* Stores the total count of entries for metadata index browsing. The count is calculated by the
* <code>json.facet</code> parameter with the following value:
*
* <pre><code>
* {
* "entries_count": {
* "type": "terms",
* "field": "facetNameField_filter",
* "limit": 0,
* "prefix": "prefix_value",
* "numBuckets": true
* }
* }
* </code></pre>
*
* This value is returned in the <code>facets</code> field of the Solr response.
*
* @param result DiscoverResult object where the total entries count will be stored
* @param solrQueryResponse QueryResponse object containing the solr response
*/
private void resolveEntriesCount(DiscoverResult result, QueryResponse solrQueryResponse) {
Object facetsObj = solrQueryResponse.getResponse().get("facets");
if (facetsObj instanceof NamedList) {
NamedList<Object> facets = (NamedList<Object>) facetsObj;
Object bucketsInfoObj = facets.get("entries_count");
if (bucketsInfoObj instanceof NamedList) {
NamedList<Object> bucketsInfo = (NamedList<Object>) bucketsInfoObj;
result.setTotalEntries((int) bucketsInfo.get("numBuckets"));
}
}
}
private void resolveFacetFields(Context context, DiscoverQuery query, DiscoverResult result,
boolean skipLoadingResponse, QueryResponse solrQueryResponse) throws SQLException {
@@ -1411,8 +1445,6 @@ public class SolrServiceImpl implements SearchService, IndexingService {
} else {
return field + "_acid";
}
} else if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_STANDARD)) {
return field;
} else {
return field;
}

31
dspace-api/src/main/java/org/dspace/discovery/indexobject/IndexFactoryImpl.java
View File

@@ -118,20 +118,10 @@ public abstract class IndexFactoryImpl<T extends IndexableObject, S> implements
ParseContext tikaContext = new ParseContext();
// Use Apache Tika to parse the full text stream(s)
boolean extractionSucceeded = false;
try (InputStream fullTextStreams = streams.getStream()) {
tikaParser.parse(fullTextStreams, tikaHandler, tikaMetadata, tikaContext);
// Write Tika metadata to "tika_meta_*" fields.
// This metadata is not very useful right now,
// but we'll keep it just in case it becomes more useful.
for (String name : tikaMetadata.names()) {
for (String value : tikaMetadata.getValues(name)) {
doc.addField("tika_meta_" + name, value);
}
}
// Save (parsed) full text to "fulltext" field
doc.addField("fulltext", tikaHandler.toString());
extractionSucceeded = true;
} catch (SAXException saxe) {
// Check if this SAXException is just a notice that this file was longer than the character limit.
// Unfortunately there is not a unique, public exception type to catch here. This error is thrown
@@ -141,6 +131,7 @@ public abstract class IndexFactoryImpl<T extends IndexableObject, S> implements
// log that we only indexed up to that configured limit
log.info("Full text is larger than the configured limit (discovery.solr.fulltext.charLimit)."
+ " Only the first {} characters were indexed.", charLimit);
extractionSucceeded = true;
} else {
log.error("Tika parsing error. Could not index full text.", saxe);
throw new IOException("Tika parsing error. Could not index full text.", saxe);
@@ -148,11 +139,19 @@ public abstract class IndexFactoryImpl<T extends IndexableObject, S> implements
} catch (TikaException | IOException ex) {
log.error("Tika parsing error. Could not index full text.", ex);
throw new IOException("Tika parsing error. Could not index full text.", ex);
} finally {
// Add document to index
solr.add(doc);
}
return;
if (extractionSucceeded) {
// Write Tika metadata to "tika_meta_*" fields.
// This metadata is not very useful right now,
// but we'll keep it just in case it becomes more useful.
for (String name : tikaMetadata.names()) {
for (String value : tikaMetadata.getValues(name)) {
doc.addField("tika_meta_" + name, value);
}
}
// Save (parsed) full text to "fulltext" field
doc.addField("fulltext", tikaHandler.toString());
}
}
// Add document to index
solr.add(doc);

8
dspace-api/src/main/java/org/dspace/discovery/indexobject/ItemIndexFactoryImpl.java
View File

@@ -154,9 +154,11 @@ public class ItemIndexFactoryImpl extends DSpaceObjectIndexFactoryImpl<Indexable
doc.addField("latestVersion", isLatestVersion(context, item));
EPerson submitter = item.getSubmitter();
if (submitter != null) {
addFacetIndex(doc, "submitter", submitter.getID().toString(),
submitter.getFullName());
if (submitter != null && !(DSpaceServicesFactory.getInstance().getConfigurationService().getBooleanProperty(
"discovery.index.item.submitter.enabled", false))) {
doc.addField("submitter_authority", submitter.getID().toString());
} else if (submitter != null) {
addFacetIndex(doc, "submitter", submitter.getID().toString(), submitter.getFullName());
}
// Add the item metadata

3
dspace-api/src/main/java/org/dspace/eperson/Group2GroupCache.java
View File

@@ -15,6 +15,7 @@ import jakarta.persistence.Id;
import jakarta.persistence.JoinColumn;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.Table;
import jakarta.persistence.UniqueConstraint;
import org.dspace.core.HibernateProxyHelper;
/**
@@ -23,7 +24,7 @@ import org.dspace.core.HibernateProxyHelper;
* @author kevinvandevelde at atmire.com
*/
@Entity
@Table(name = "group2groupcache")
@Table(name = "group2groupcache", uniqueConstraints = { @UniqueConstraint(columnNames = {"parent_id", "child_id"}) })
public class Group2GroupCache implements Serializable {
@Id

76
dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java
View File

@@ -20,6 +20,7 @@ import java.util.Set;
import java.util.UUID;
import org.apache.commons.collections4.CollectionUtils;
import org.apache.commons.collections4.SetUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.logging.log4j.LogManager;
@@ -673,15 +674,14 @@ public class GroupServiceImpl extends DSpaceObjectServiceImpl<Group> implements
/**
* Regenerate the group cache AKA the group2groupcache table in the database -
* meant to be called when a group is added or removed from another group
* Returns a set with pairs of parent and child group UUIDs, representing the new cache table rows.
*
* @param context The relevant DSpace Context.
* @param flushQueries flushQueries Flush all pending queries
* @param context The relevant DSpace Context.
* @param flushQueries flushQueries Flush all pending queries
* @return Pairs of parent and child group UUID of the new cache.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
protected void rethinkGroupCache(Context context, boolean flushQueries) throws SQLException {
private Set<Pair<UUID, UUID>> computeNewCache(Context context, boolean flushQueries) throws SQLException {
Map<UUID, Set<UUID>> parents = new HashMap<>();
List<Pair<UUID, UUID>> group2groupResults = groupDAO.getGroup2GroupResults(context, flushQueries);
@@ -689,19 +689,8 @@ public class GroupServiceImpl extends DSpaceObjectServiceImpl<Group> implements
UUID parent = group2groupResult.getLeft();
UUID child = group2groupResult.getRight();
// if parent doesn't have an entry, create one
if (!parents.containsKey(parent)) {
Set<UUID> children = new HashSet<>();
// add child id to the list
children.add(child);
parents.put(parent, children);
} else {
// parent has an entry, now add the child to the parent's record
// of children
Set<UUID> children = parents.get(parent);
children.add(child);
}
parents.putIfAbsent(parent, new HashSet<>());
parents.get(parent).add(child);
}
// now parents is a hash of all of the IDs of groups that are parents
@@ -714,28 +703,43 @@ public class GroupServiceImpl extends DSpaceObjectServiceImpl<Group> implements
parent.getValue().addAll(myChildren);
}
// empty out group2groupcache table
group2GroupCacheDAO.deleteAll(context);
// write out new one
// write out new cache IN MEMORY ONLY and returns it
Set<Pair<UUID, UUID>> newCache = new HashSet<>();
for (Map.Entry<UUID, Set<UUID>> parent : parents.entrySet()) {
UUID key = parent.getKey();
for (UUID child : parent.getValue()) {
Group parentGroup = find(context, key);
Group childGroup = find(context, child);
if (parentGroup != null && childGroup != null && group2GroupCacheDAO
.find(context, parentGroup, childGroup) == null) {
Group2GroupCache group2GroupCache = group2GroupCacheDAO.create(context, new Group2GroupCache());
group2GroupCache.setParent(parentGroup);
group2GroupCache.setChild(childGroup);
group2GroupCacheDAO.save(context, group2GroupCache);
}
newCache.add(Pair.of(key, child));
}
}
return newCache;
}
/**
* Regenerate the group cache AKA the group2groupcache table in the database -
* meant to be called when a group is added or removed from another group
*
* @param context The relevant DSpace Context.
* @param flushQueries flushQueries Flush all pending queries
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
protected void rethinkGroupCache(Context context, boolean flushQueries) throws SQLException {
// current cache in the database
Set<Pair<UUID, UUID>> oldCache = group2GroupCacheDAO.getCache(context);
// correct cache, computed from the Group table
Set<Pair<UUID, UUID>> newCache = computeNewCache(context, flushQueries);
SetUtils.SetView<Pair<UUID, UUID>> toDelete = SetUtils.difference(oldCache, newCache);
SetUtils.SetView<Pair<UUID, UUID>> toCreate = SetUtils.difference(newCache, oldCache);
for (Pair<UUID, UUID> pair : toDelete ) {
group2GroupCacheDAO.deleteFromCache(context, pair.getLeft(), pair.getRight());
}
for (Pair<UUID, UUID> pair : toCreate ) {
group2GroupCacheDAO.addToCache(context, pair.getLeft(), pair.getRight());
}
}
@Override

74
dspace-api/src/main/java/org/dspace/eperson/dao/Group2GroupCacheDAO.java
View File

@@ -9,7 +9,10 @@ package org.dspace.eperson.dao;
import java.sql.SQLException;
import java.util.List;
import java.util.Set;
import java.util.UUID;
import org.apache.commons.lang3.tuple.Pair;
import org.dspace.core.Context;
import org.dspace.core.GenericDAO;
import org.dspace.eperson.Group;
@@ -25,13 +28,74 @@ import org.dspace.eperson.Group2GroupCache;
*/
public interface Group2GroupCacheDAO extends GenericDAO<Group2GroupCache> {
public List<Group2GroupCache> findByParent(Context context, Group group) throws SQLException;
/**
* Returns the current cache table as a set of UUID pairs.
* @param context The relevant DSpace Context.
* @return Set of UUID pairs, where the first element is the parent UUID and the second one is the child UUID.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
Set<Pair<UUID, UUID>> getCache(Context context) throws SQLException;
public List<Group2GroupCache> findByChildren(Context context, Iterable<Group> groups) throws SQLException;
/**
* Returns all cache entities that are children of a given parent Group entity.
* @param context The relevant DSpace Context.
* @param group Parent group to perform the search.
* @return List of cached groups that are children of the parent group.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
List<Group2GroupCache> findByParent(Context context, Group group) throws SQLException;
public Group2GroupCache findByParentAndChild(Context context, Group parent, Group child) throws SQLException;
/**
* Returns all cache entities that are parents of at least one group from a children groups list.
* @param context The relevant DSpace Context.
* @param groups Children groups to perform the search.
* @return List of cached groups that are parents of at least one group from the children groups list.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
List<Group2GroupCache> findByChildren(Context context, Iterable<Group> groups) throws SQLException;
public Group2GroupCache find(Context context, Group parent, Group child) throws SQLException;
/**
* Returns the cache entity given specific parent and child groups.
* @param context The relevant DSpace Context.
* @param parent Parent group.
* @param child Child gruoup.
* @return Cached group.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
Group2GroupCache findByParentAndChild(Context context, Group parent, Group child) throws SQLException;
public void deleteAll(Context context) throws SQLException;
/**
* Returns the cache entity given specific parent and child groups.
* @param context The relevant DSpace Context.
* @param parent Parent group.
* @param child Child gruoup.
* @return Cached group.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
Group2GroupCache find(Context context, Group parent, Group child) throws SQLException;
/**
* Completely deletes the current cache table.
* @param context The relevant DSpace Context.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
void deleteAll(Context context) throws SQLException;
/**
* Deletes a specific cache row given parent and child groups UUIDs.
* @param context The relevant DSpace Context.
* @param parent Parent group UUID.
* @param child Child group UUID.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
void deleteFromCache(Context context, UUID parent, UUID child) throws SQLException;
/**
* Adds a single row to the cache table given parent and child groups UUIDs.
* @param context The relevant DSpace Context.
* @param parent Parent group UUID.
* @param child Child group UUID.
* @throws SQLException An exception that provides information on a database access error or other errors.
*/
void addToCache(Context context, UUID parent, UUID child) throws SQLException;
}

34
dspace-api/src/main/java/org/dspace/eperson/dao/impl/Group2GroupCacheDAOImpl.java
View File

@@ -8,14 +8,18 @@
package org.dspace.eperson.dao.impl;
import java.sql.SQLException;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Set;
import java.util.UUID;
import jakarta.persistence.Query;
import jakarta.persistence.criteria.CriteriaBuilder;
import jakarta.persistence.criteria.CriteriaQuery;
import jakarta.persistence.criteria.Predicate;
import jakarta.persistence.criteria.Root;
import org.apache.commons.lang3.tuple.Pair;
import org.dspace.core.AbstractHibernateDAO;
import org.dspace.core.Context;
import org.dspace.eperson.Group;
@@ -35,6 +39,16 @@ public class Group2GroupCacheDAOImpl extends AbstractHibernateDAO<Group2GroupCac
super();
}
@Override
public Set<Pair<UUID, UUID>> getCache(Context context) throws SQLException {
Query query = createQuery(
context,
"SELECT new org.apache.commons.lang3.tuple.ImmutablePair(g.parent.id, g.child.id) FROM Group2GroupCache g"
);
List<Pair<UUID, UUID>> results = query.getResultList();
return new HashSet<Pair<UUID, UUID>>(results);
}
@Override
public List<Group2GroupCache> findByParent(Context context, Group group) throws SQLException {
CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
@@ -90,4 +104,24 @@ public class Group2GroupCacheDAOImpl extends AbstractHibernateDAO<Group2GroupCac
public void deleteAll(Context context) throws SQLException {
createQuery(context, "delete from Group2GroupCache").executeUpdate();
}
@Override
public void deleteFromCache(Context context, UUID parent, UUID child) throws SQLException {
Query query = getHibernateSession(context).createNativeQuery(
"delete from group2groupcache g WHERE g.parent_id = :parent AND g.child_id = :child"
);
query.setParameter("parent", parent);
query.setParameter("child", child);
query.executeUpdate();
}
@Override
public void addToCache(Context context, UUID parent, UUID child) throws SQLException {
Query query = getHibernateSession(context).createNativeQuery(
"insert into group2groupcache (parent_id, child_id) VALUES (:parent, :child)"
);
query.setParameter("parent", parent);
query.setParameter("child", child);
query.executeUpdate();
}
}

144
dspace-api/src/main/java/org/dspace/google/GoogleAccount.java
View File

@@ -1,144 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.google;
import java.io.File;
import java.util.HashSet;
import java.util.Set;
import com.google.api.client.auth.oauth2.Credential;
import com.google.api.client.googleapis.auth.oauth2.GoogleCredential;
import com.google.api.client.googleapis.javanet.GoogleNetHttpTransport;
import com.google.api.client.http.HttpTransport;
import com.google.api.client.json.JsonFactory;
import com.google.api.client.json.jackson2.JacksonFactory;
import com.google.api.services.analytics.Analytics;
import com.google.api.services.analytics.AnalyticsScopes;
import org.apache.logging.log4j.Logger;
import org.dspace.services.factory.DSpaceServicesFactory;
/**
* User: Robin Taylor
* Date: 11/07/2014
* Time: 13:23
*/
public class GoogleAccount {
// Read from config
private String applicationName;
private String tableId;
private String emailAddress;
private String certificateLocation;
// Created from factories
private JsonFactory jsonFactory;
private HttpTransport httpTransport;
// The Google stuff
private Credential credential;
private Analytics client;
private volatile static GoogleAccount uniqueInstance;
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(GoogleAccount.class);
private GoogleAccount() {
applicationName = DSpaceServicesFactory.getInstance().getConfigurationService()
.getProperty("google-analytics.application.name");
tableId = DSpaceServicesFactory.getInstance().getConfigurationService()
.getProperty("google-analytics.table.id");
emailAddress = DSpaceServicesFactory.getInstance().getConfigurationService()
.getProperty("google-analytics.account.email");
certificateLocation = DSpaceServicesFactory.getInstance().getConfigurationService()
.getProperty("google-analytics.certificate.location");
jsonFactory = JacksonFactory.getDefaultInstance();
try {
httpTransport = GoogleNetHttpTransport.newTrustedTransport();
credential = authorize();
} catch (Exception e) {
throw new RuntimeException("Error initialising Google Analytics client", e);
}
// Create an Analytics instance
client = new Analytics.Builder(httpTransport, jsonFactory, credential).setApplicationName(applicationName)
.build();
log.info("Google Analytics client successfully initialised");
}
public static GoogleAccount getInstance() {
if (uniqueInstance == null) {
synchronized (GoogleAccount.class) {
if (uniqueInstance == null) {
uniqueInstance = new GoogleAccount();
}
}
}
return uniqueInstance;
}
private Credential authorize() throws Exception {
Set<String> scopes = new HashSet<String>();
scopes.add(AnalyticsScopes.ANALYTICS);
scopes.add(AnalyticsScopes.ANALYTICS_EDIT);
scopes.add(AnalyticsScopes.ANALYTICS_MANAGE_USERS);
scopes.add(AnalyticsScopes.ANALYTICS_PROVISION);
scopes.add(AnalyticsScopes.ANALYTICS_READONLY);
credential = new GoogleCredential.Builder()
.setTransport(httpTransport)
.setJsonFactory(jsonFactory)
.setServiceAccountId(emailAddress)
.setServiceAccountScopes(scopes)
.setServiceAccountPrivateKeyFromP12File(new File(certificateLocation))
.build();
return credential;
}
public String getApplicationName() {
return applicationName;
}
public String getTableId() {
return tableId;
}
public String getEmailAddress() {
return emailAddress;
}
public String getCertificateLocation() {
return certificateLocation;
}
public JsonFactory getJsonFactory() {
return jsonFactory;
}
public HttpTransport getHttpTransport() {
return httpTransport;
}
public Credential getCredential() {
return credential;
}
public Analytics getClient() {
return client;
}
}

49
dspace-api/src/main/java/org/dspace/google/GoogleQueryManager.java
View File

@@ -1,49 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.google;
import java.io.IOException;
import com.google.api.services.analytics.model.GaData;
/**
* User: Robin Taylor
* Date: 20/08/2014
* Time: 09:26
*/
public class GoogleQueryManager {
public GaData getPageViews(String startDate, String endDate, String handle) throws IOException {
return GoogleAccount.getInstance().getClient().data().ga().get(
GoogleAccount.getInstance().getTableId(),
startDate,
endDate,
"ga:pageviews") // Metrics.
.setDimensions("ga:year,ga:month")
.setSort("-ga:year,-ga:month")
.setFilters("ga:pagePath=~/handle/" + handle + "$")
.execute();
}
public GaData getBitstreamDownloads(String startDate, String endDate, String handle) throws IOException {
return GoogleAccount.getInstance().getClient().data().ga().get(
GoogleAccount.getInstance().getTableId(),
startDate,
endDate,
"ga:totalEvents") // Metrics.
.setDimensions("ga:year,ga:month")
.setSort("-ga:year,-ga:month")
.setFilters(
"ga:eventCategory==bitstream;ga:eventAction==download;ga:pagePath=~" + handle + "/")
.execute();
}
}

201
dspace-api/src/main/java/org/dspace/google/GoogleRecorderEventListener.java
View File

@@ -1,201 +0,0 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.google;
import java.io.IOException;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import jakarta.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
import org.apache.http.NameValuePair;
import org.apache.http.client.entity.UrlEncodedFormEntity;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClients;
import org.apache.http.message.BasicNameValuePair;
import org.apache.logging.log4j.Logger;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.core.Constants;
import org.dspace.service.ClientInfoService;
import org.dspace.services.ConfigurationService;
import org.dspace.services.model.Event;
import org.dspace.usage.AbstractUsageEventListener;
import org.dspace.usage.UsageEvent;
import org.springframework.beans.factory.annotation.Autowired;
/**
* User: Robin Taylor
* Date: 14/08/2014
* Time: 10:05
*
* Notify Google Analytics of... well anything we want really.
* @deprecated Use org.dspace.google.GoogleAsyncEventListener instead
*/
@Deprecated
public class GoogleRecorderEventListener extends AbstractUsageEventListener {
private String analyticsKey;
private CloseableHttpClient httpclient;
private String GoogleURL = "https://www.google-analytics.com/collect";
private static Logger log = org.apache.logging.log4j.LogManager.getLogger(GoogleRecorderEventListener.class);
protected ContentServiceFactory contentServiceFactory;
protected ConfigurationService configurationService;
protected ClientInfoService clientInfoService;
public GoogleRecorderEventListener() {
// httpclient is threadsafe so we only need one.
httpclient = HttpClients.createDefault();
}
@Autowired
public void setContentServiceFactory(ContentServiceFactory contentServiceFactory) {
this.contentServiceFactory = contentServiceFactory;
}
@Autowired
public void setConfigurationService(ConfigurationService configurationService) {
this.configurationService = configurationService;
}
@Autowired
public void setClientInfoService(ClientInfoService clientInfoService) {
this.clientInfoService = clientInfoService;
}
@Override
public void receiveEvent(Event event) {
if ((event instanceof UsageEvent)) {
log.debug("Usage event received " + event.getName());
// This is a wee bit messy but these keys should be combined in future.
analyticsKey = configurationService.getProperty("google.analytics.key");
if (StringUtils.isNotBlank(analyticsKey)) {
try {
UsageEvent ue = (UsageEvent) event;
if (ue.getAction() == UsageEvent.Action.VIEW) {
if (ue.getObject().getType() == Constants.BITSTREAM) {
logEvent(ue, "bitstream", "download");
// Note: I've left this commented out code here to show how we could record page views
// as events,
// but since they are already taken care of by the Google Analytics Javascript there is
// not much point.
//} else if (ue.getObject().getType() == Constants.ITEM) {
// logEvent(ue, "item", "view");
//} else if (ue.getObject().getType() == Constants.COLLECTION) {
// logEvent(ue, "collection", "view");
//} else if (ue.getObject().getType() == Constants.COMMUNITY) {
// logEvent(ue, "community", "view");
}
}
} catch (Exception e) {
log.error(e.getMessage());
}
}
}
}
private void logEvent(UsageEvent ue, String category, String action) throws IOException, SQLException {
HttpPost httpPost = new HttpPost(GoogleURL);
List<NameValuePair> nvps = new ArrayList<NameValuePair>();
nvps.add(new BasicNameValuePair("v", "1"));
nvps.add(new BasicNameValuePair("tid", analyticsKey));
// Client Id, should uniquely identify the user or device. If we have a session id for the user
// then lets use it, else generate a UUID.
if (ue.getRequest().getSession(false) != null) {
nvps.add(new BasicNameValuePair("cid", ue.getRequest().getSession().getId()));
} else {
nvps.add(new BasicNameValuePair("cid", UUID.randomUUID().toString()));
}
nvps.add(new BasicNameValuePair("t", "event"));
nvps.add(new BasicNameValuePair("uip", getIPAddress(ue.getRequest())));
nvps.add(new BasicNameValuePair("ua", ue.getRequest().getHeader("USER-AGENT")));
nvps.add(new BasicNameValuePair("dr", ue.getRequest().getHeader("referer")));
nvps.add(new BasicNameValuePair("dp", ue.getRequest().getRequestURI()));
nvps.add(new BasicNameValuePair("dt", getObjectName(ue)));
nvps.add(new BasicNameValuePair("ec", category));
nvps.add(new BasicNameValuePair("ea", action));
if (ue.getObject().getType() == Constants.BITSTREAM) {
// Bitstream downloads may occasionally be for collection or community images, so we need to label them
// with the parent object type.
nvps.add(new BasicNameValuePair("el", getParentType(ue)));
}
httpPost.setEntity(new UrlEncodedFormEntity(nvps));
try (CloseableHttpResponse response2 = httpclient.execute(httpPost)) {
// I can't find a list of what are acceptable responses, so I log the response but take no action.
log.debug("Google Analytics response is " + response2.getStatusLine());
}
log.debug("Posted to Google Analytics - " + ue.getRequest().getRequestURI());
}
private String getParentType(UsageEvent ue) {
try {
int parentType = contentServiceFactory.getDSpaceObjectService(ue.getObject())
.getParentObject(ue.getContext(), ue.getObject()).getType();
if (parentType == Constants.ITEM) {
return "item";
} else if (parentType == Constants.COLLECTION) {
return "collection";
} else if (parentType == Constants.COMMUNITY) {
return "community";
}
} catch (SQLException e) {
// This shouldn't merit interrupting the user's transaction so log the error and continue.
log.error(
"Error in Google Analytics recording - can't determine ParentObjectType for bitstream " + ue.getObject()
.getID());
e.printStackTrace();
}
return null;
}
private String getObjectName(UsageEvent ue) {
try {
if (ue.getObject().getType() == Constants.BITSTREAM) {
// For a bitstream download we really want to know the title of the owning item rather than the
// bitstream name.
return contentServiceFactory.getDSpaceObjectService(ue.getObject())
.getParentObject(ue.getContext(), ue.getObject()).getName();
} else {
return ue.getObject().getName();
}
} catch (SQLException e) {
// This shouldn't merit interrupting the user's transaction so log the error and continue.
log.error(
"Error in Google Analytics recording - can't determine ParentObjectName for bitstream " + ue.getObject()
.getID());
e.printStackTrace();
}
return null;
}
private String getIPAddress(HttpServletRequest request) {
return clientInfoService.getClientIp(request);
}
}

5
dspace-api/src/main/java/org/dspace/identifier/IdentifierServiceImpl.java
View File

@@ -57,6 +57,11 @@ public class IdentifierServiceImpl implements IdentifierService {
}
}
@Override
public List<IdentifierProvider> getProviders() {
return this.providers;
}
/**
* Reserves identifiers for the item
*

3
dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java
View File

@@ -577,7 +577,8 @@ public class DOIOrganiser {
}
} catch (IdentifierException ex) {
if (!(ex instanceof DOIIdentifierException)) {
LOG.error("It wasn't possible to register the identifier online. ", ex);
LOG.error("Registering DOI {} for object {}: the registrar returned an error.",
doiRow.getDoi(), dso.getID(), ex);
}
DOIIdentifierException doiIdentifierException = (DOIIdentifierException) ex;

22
dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java
View File

@@ -461,6 +461,10 @@ public class DataCiteConnector
log.warn("While reserving the DOI {}, we got a http status code "
+ "{} and the message \"{}\".",
doi, Integer.toString(resp.statusCode), resp.getContent());
Format format = Format.getCompactFormat();
format.setEncoding("UTF-8");
XMLOutputter xout = new XMLOutputter(format);
log.info("We send the following XML:\n{}", xout.outputString(root));
throw new DOIIdentifierException("Unable to parse an answer from "
+ "DataCite API. Please have a look into DSpace logs.",
DOIIdentifierException.BAD_ANSWER);
@@ -632,6 +636,14 @@ public class DataCiteConnector
return sendHttpRequest(httpget, doi);
}
/**
* Send a DataCite metadata document to the registrar.
*
* @param doi identify the object.
* @param metadataRoot describe the object. The root element of the document.
* @return the registrar's response.
* @throws DOIIdentifierException passed through.
*/
protected DataCiteResponse sendMetadataPostRequest(String doi, Element metadataRoot)
throws DOIIdentifierException {
Format format = Format.getCompactFormat();
@@ -640,6 +652,14 @@ public class DataCiteConnector
return sendMetadataPostRequest(doi, xout.outputString(new Document(metadataRoot)));
}
/**
* Send a DataCite metadata document to the registrar.
*
* @param doi identify the object.
* @param metadata describe the object.
* @return the registrar's response.
* @throws DOIIdentifierException passed through.
*/
protected DataCiteResponse sendMetadataPostRequest(String doi, String metadata)
throws DOIIdentifierException {
// post mds/metadata/
@@ -687,7 +707,7 @@ public class DataCiteConnector
* properties such as request URI and method type.
* @param doi DOI string to operate on
* @return response from DataCite
* @throws DOIIdentifierException if DOI error
* @throws DOIIdentifierException if registrar returns an error.
*/
protected DataCiteResponse sendHttpRequest(HttpUriRequest req, String doi)
throws DOIIdentifierException {

6
dspace-api/src/main/java/org/dspace/identifier/service/IdentifierService.java
View File

@@ -19,6 +19,7 @@ import org.dspace.identifier.Identifier;
import org.dspace.identifier.IdentifierException;
import org.dspace.identifier.IdentifierNotFoundException;
import org.dspace.identifier.IdentifierNotResolvableException;
import org.dspace.identifier.IdentifierProvider;
/**
* @author Fabio Bolognesi (fabio at atmire dot com)
@@ -194,4 +195,9 @@ public interface IdentifierService {
void delete(Context context, DSpaceObject dso, String identifier)
throws AuthorizeException, SQLException, IdentifierException;
/**
* Get List of currently enabled IdentifierProviders
* @return List of enabled IdentifierProvider objects.
*/
List<IdentifierProvider> getProviders();
}

2
dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/SimpleConcatContributor.java vendored
View File

@@ -26,7 +26,7 @@ import org.jdom2.xpath.XPathFactory;
* This contributor is able to concat multi value.
* Given a certain path, if it contains several nodes,
* the values of nodes will be concatenated into a single one.
* The concrete example we can see in the file wos-responce.xml in the <abstract_text> node,
* The concrete example we can see in the file wos-response.xml in the <abstract_text> node,
* which may contain several <p> paragraphs,
* this Contributor allows concatenating all <p> paragraphs. to obtain a single one.
*

8
dspace-api/src/main/java/org/dspace/orcid/client/OrcidClient.java
View File

@@ -10,6 +10,7 @@ package org.dspace.orcid.client;
import java.util.List;
import java.util.Optional;
import org.dspace.orcid.OrcidToken;
import org.dspace.orcid.exception.OrcidClientException;
import org.dspace.orcid.model.OrcidTokenResponseDTO;
import org.orcid.jaxb.model.v3.release.record.Person;
@@ -161,4 +162,11 @@ public interface OrcidClient {
*/
OrcidResponse deleteByPutCode(String accessToken, String orcid, String putCode, String path);
/**
* Revokes the given {@param accessToken} with a POST method.
* @param orcidToken the access token to revoke
* @throws OrcidClientException if some error occurs during the search
*/
void revokeToken(OrcidToken orcidToken);
}

37
dspace-api/src/main/java/org/dspace/orcid/client/OrcidClientImpl.java
View File

@@ -42,6 +42,7 @@ import org.apache.http.client.methods.RequestBuilder;
import org.apache.http.entity.StringEntity;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.message.BasicNameValuePair;
import org.dspace.orcid.OrcidToken;
import org.dspace.orcid.exception.OrcidClientException;
import org.dspace.orcid.model.OrcidEntityType;
import org.dspace.orcid.model.OrcidProfileSectionType;
@@ -178,6 +179,16 @@ public class OrcidClientImpl implements OrcidClient {
return execute(buildDeleteUriRequest(accessToken, "/" + orcid + path + "/" + putCode), true);
}
@Override
public void revokeToken(OrcidToken orcidToken) {
List<NameValuePair> params = new ArrayList<>();
params.add(new BasicNameValuePair("client_id", orcidConfiguration.getClientId()));
params.add(new BasicNameValuePair("client_secret", orcidConfiguration.getClientSecret()));
params.add(new BasicNameValuePair("token", orcidToken.getAccessToken()));
executeSuccessful(buildPostForRevokeToken(new UrlEncodedFormEntity(params, Charset.defaultCharset())));
}
@Override
public OrcidTokenResponseDTO getReadPublicAccessToken() {
return getClientCredentialsAccessToken("/read-public");
@@ -220,6 +231,14 @@ public class OrcidClientImpl implements OrcidClient {
.build();
}
private HttpUriRequest buildPostForRevokeToken(HttpEntity entity) {
return post(orcidConfiguration.getRevokeUrl())
.addHeader("Accept", "application/json")
.addHeader("Content-Type", "application/x-www-form-urlencoded")
.setEntity(entity)
.build();
}
private HttpUriRequest buildPutUriRequest(String accessToken, String relativePath, Object object) {
return put(orcidConfiguration.getApiUrl() + relativePath.trim())
.addHeader("Content-Type", "application/vnd.orcid+xml")
@@ -234,6 +253,24 @@ public class OrcidClientImpl implements OrcidClient {
.build();
}
private void executeSuccessful(HttpUriRequest httpUriRequest) {
try {
HttpClient client = HttpClientBuilder.create().build();
HttpResponse response = client.execute(httpUriRequest);
if (isNotSuccessfull(response)) {
throw new OrcidClientException(
getStatusCode(response),
"Operation " + httpUriRequest.getMethod() + " for the resource " + httpUriRequest.getURI() +
" was not successful: " + new String(response.getEntity().getContent().readAllBytes(),
StandardCharsets.UTF_8)
);
}
} catch (IOException e) {
throw new RuntimeException(e);
}
}
private <T> T executeAndParseJson(HttpUriRequest httpUriRequest, Class<T> clazz) {
HttpClient client = HttpClientBuilder.create().build();

9
dspace-api/src/main/java/org/dspace/orcid/client/OrcidConfiguration.java
View File

@@ -35,6 +35,8 @@ public final class OrcidConfiguration {
private String scopes;
private String revokeUrl;
public String getApiUrl() {
return apiUrl;
}
@@ -111,4 +113,11 @@ public final class OrcidConfiguration {
return !StringUtils.isAnyBlank(clientId, clientSecret);
}
public String getRevokeUrl() {
return revokeUrl;
}
public void setRevokeUrl(String revokeUrl) {
this.revokeUrl = revokeUrl;
}
}

39
dspace-api/src/main/java/org/dspace/orcid/service/impl/OrcidSynchronizationServiceImpl.java
View File

@@ -37,6 +37,7 @@ import org.dspace.discovery.indexobject.IndexableItem;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.service.EPersonService;
import org.dspace.orcid.OrcidToken;
import org.dspace.orcid.client.OrcidClient;
import org.dspace.orcid.model.OrcidEntityType;
import org.dspace.orcid.model.OrcidTokenResponseDTO;
import org.dspace.orcid.service.OrcidSynchronizationService;
@@ -47,6 +48,8 @@ import org.dspace.profile.OrcidProfileSyncPreference;
import org.dspace.profile.OrcidSynchronizationMode;
import org.dspace.profile.service.ResearcherProfileService;
import org.dspace.services.ConfigurationService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
/**
@@ -57,6 +60,7 @@ import org.springframework.beans.factory.annotation.Autowired;
*/
public class OrcidSynchronizationServiceImpl implements OrcidSynchronizationService {
private static final Logger log = LoggerFactory.getLogger(OrcidSynchronizationServiceImpl.class);
@Autowired
private ItemService itemService;
@@ -75,6 +79,9 @@ public class OrcidSynchronizationServiceImpl implements OrcidSynchronizationServ
@Autowired
private ResearcherProfileService researcherProfileService;
@Autowired
private OrcidClient orcidClient;
@Override
public void linkProfile(Context context, Item profile, OrcidTokenResponseDTO token) throws SQLException {
@@ -114,20 +121,33 @@ public class OrcidSynchronizationServiceImpl implements OrcidSynchronizationServ
@Override
public void unlinkProfile(Context context, Item profile) throws SQLException {
itemService.clearMetadata(context, profile, "person", "identifier", "orcid", Item.ANY);
itemService.clearMetadata(context, profile, "dspace", "orcid", "scope", Item.ANY);
itemService.clearMetadata(context, profile, "dspace", "orcid", "authenticated", Item.ANY);
clearOrcidProfileMetadata(context, profile);
if (!configurationService.getBooleanProperty("orcid.disconnection.remain-sync", false)) {
clearSynchronizationSettings(context, profile);
}
clearSynchronizationSettings(context, profile);
orcidTokenService.deleteByProfileItem(context, profile);
clearOrcidToken(context, profile);
updateItem(context, profile);
}
private void clearOrcidToken(Context context, Item profile) {
OrcidToken profileToken = orcidTokenService.findByProfileItem(context, profile);
if (profileToken == null) {
log.warn("Cannot find any token related to the user profile: {}", profile.getID());
return;
}
orcidTokenService.deleteByProfileItem(context, profile);
orcidClient.revokeToken(profileToken);
}
private void clearOrcidProfileMetadata(Context context, Item profile) throws SQLException {
itemService.clearMetadata(context, profile, "person", "identifier", "orcid", Item.ANY);
itemService.clearMetadata(context, profile, "dspace", "orcid", "scope", Item.ANY);
itemService.clearMetadata(context, profile, "dspace", "orcid", "authenticated", Item.ANY);
}
@Override
public boolean setEntityPreference(Context context, Item profile, OrcidEntityType type,
OrcidEntitySyncPreference value) throws SQLException {
@@ -273,6 +293,11 @@ public class OrcidSynchronizationServiceImpl implements OrcidSynchronizationServ
private void clearSynchronizationSettings(Context context, Item profile)
throws SQLException {
if (configurationService.getBooleanProperty("orcid.disconnection.remain-sync", false)) {
return;
}
itemService.clearMetadata(context, profile, "dspace", "orcid", "sync-mode", Item.ANY);
itemService.clearMetadata(context, profile, "dspace", "orcid", "sync-profile", Item.ANY);

2
dspace-api/src/main/java/org/dspace/rdf/RDFConsumer.java
View File

@@ -243,7 +243,7 @@ public class RDFConsumer implements Consumer {
DSOIdentifier id = new DSOIdentifier(dso, ctx);
// If an item gets withdrawn, a MODIFY event is fired. We have to
// delete the item from the triple store instead of converting it.
// we don't have to take care for reinstantions of items as they can
// we don't have to take care for reinstate events on items as they can
// be processed as normal modify events.
if (dso instanceof Item
&& event.getDetail() != null

64
dspace-api/src/main/java/org/dspace/scripts/ProcessServiceImpl.java
View File

@@ -45,14 +45,15 @@ import org.dspace.core.Context;
import org.dspace.core.LogHelper;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.eperson.service.EPersonService;
import org.dspace.scripts.service.ProcessService;
import org.dspace.services.ConfigurationService;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
/**
* The implementation for the {@link ProcessService} class
*/
public class ProcessServiceImpl implements ProcessService {
public class ProcessServiceImpl implements ProcessService, InitializingBean {
private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(ProcessService.class);
@@ -72,7 +73,34 @@ public class ProcessServiceImpl implements ProcessService {
private MetadataFieldService metadataFieldService;
@Autowired
private EPersonService ePersonService;
private ConfigurationService configurationService;
@Override
public void afterPropertiesSet() throws Exception {
try {
Context context = new Context();
// Processes that were running or scheduled when tomcat crashed, should be cleaned up during startup.
List<Process> processesToBeFailed = findByStatusAndCreationTimeOlderThan(
context, List.of(ProcessStatus.RUNNING, ProcessStatus.SCHEDULED), new Date());
for (Process process : processesToBeFailed) {
context.setCurrentUser(process.getEPerson());
// Fail the process.
log.info("Process with ID {} did not complete before tomcat shutdown, failing it now.",
process.getID());
fail(context, process);
// But still attach its log to the process.
appendLog(process.getID(), process.getName(),
"Process did not complete before tomcat shutdown.",
ProcessLogLevel.ERROR);
createLogBitstream(context, process);
}
context.complete();
} catch (Exception e) {
log.error("Unable to clean up Processes: ", e);
}
}
@Override
public Process create(Context context, EPerson ePerson, String scriptName,
@@ -293,8 +321,8 @@ public class ProcessServiceImpl implements ProcessService {
@Override
public void appendLog(int processId, String scriptName, String output, ProcessLogLevel processLogLevel)
throws IOException {
File tmpDir = FileUtils.getTempDirectory();
File tempFile = new File(tmpDir, scriptName + processId + ".log");
File logsDir = getLogsDirectory();
File tempFile = new File(logsDir, processId + "-" + scriptName + ".log");
FileWriter out = new FileWriter(tempFile, true);
try {
try (BufferedWriter writer = new BufferedWriter(out)) {
@@ -309,12 +337,15 @@ public class ProcessServiceImpl implements ProcessService {
@Override
public void createLogBitstream(Context context, Process process)
throws IOException, SQLException, AuthorizeException {
File tmpDir = FileUtils.getTempDirectory();
File tempFile = new File(tmpDir, process.getName() + process.getID() + ".log");
FileInputStream inputStream = FileUtils.openInputStream(tempFile);
appendFile(context, process, inputStream, Process.OUTPUT_TYPE, process.getName() + process.getID() + ".log");
inputStream.close();
tempFile.delete();
File logsDir = getLogsDirectory();
File tempFile = new File(logsDir, process.getID() + "-" + process.getName() + ".log");
if (tempFile.exists()) {
FileInputStream inputStream = FileUtils.openInputStream(tempFile);
appendFile(context, process, inputStream, Process.OUTPUT_TYPE,
process.getID() + "-" + process.getName() + ".log");
inputStream.close();
tempFile.delete();
}
}
@Override
@@ -343,4 +374,15 @@ public class ProcessServiceImpl implements ProcessService {
return sb.toString();
}
private File getLogsDirectory() {
String pathStr = configurationService.getProperty("dspace.dir")
+ File.separator + "log" + File.separator + "processes";
File logsDir = new File(pathStr);
if (!logsDir.exists()) {
if (!logsDir.mkdirs()) {
throw new RuntimeException("Couldn't create [dspace.dir]/log/processes/ directory.");
}
}
return logsDir;
}
}

11
dspace-api/src/main/java/org/dspace/statistics/util/StatisticsImporter.java
View File

@@ -357,7 +357,7 @@ public class StatisticsImporter {
SolrInputDocument sid = new SolrInputDocument();
sid.addField("ip", ip);
sid.addField("type", dso.getType());
sid.addField("id", dso.getID());
sid.addField("id", dso.getID().toString());
sid.addField("time", DateFormatUtils.format(date, SolrLoggerServiceImpl.DATE_FORMAT_8601));
sid.addField("continent", continent);
sid.addField("country", country);
@@ -471,13 +471,13 @@ public class StatisticsImporter {
boolean verbose = line.hasOption('v');
// Find our solr server
String sserver = configurationService.getProperty("solr-statistics", "server");
String sserver = configurationService.getProperty("solr-statistics.server");
if (verbose) {
System.out.println("Writing to solr server at: " + sserver);
}
solr = new HttpSolrClient.Builder(sserver).build();
String dbPath = configurationService.getProperty("usage-statistics", "dbfile");
String dbPath = configurationService.getProperty("usage-statistics.dbfile");
try {
File dbFile = new File(dbPath);
geoipLookup = new DatabaseReader.Builder(dbFile).build();
@@ -492,6 +492,11 @@ public class StatisticsImporter {
"Unable to load GeoLite Database file (" + dbPath + ")! You may need to reinstall it. See the DSpace " +
"installation instructions for more details.",
e);
} catch (NullPointerException e) {
log.error(
"The value of the property usage-statistics.dbfile is null. You may need to install the GeoLite " +
"Database file and/or uncomment the property in the config file!",
e);
}

2
dspace-api/src/main/java/org/dspace/usage/package-info.java
View File

@@ -25,7 +25,7 @@
* {@code EventService}, as with the stock listeners.
* </p>
*
* @see org.dspace.google.GoogleRecorderEventListener
* @see org.dspace.google.GoogleAsyncEventListener
* @see org.dspace.statistics.SolrLoggerUsageEventListener
*/

15
dspace-api/src/main/java/org/dspace/xmlworkflow/state/actions/processingaction/ScoreReviewAction.java
View File

@@ -8,6 +8,7 @@
package org.dspace.xmlworkflow.state.actions.processingaction;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
@@ -20,6 +21,8 @@ import org.dspace.app.util.Util;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.MetadataFieldName;
import org.dspace.core.Context;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.xmlworkflow.service.WorkflowRequirementsService;
import org.dspace.xmlworkflow.state.Step;
import org.dspace.xmlworkflow.state.actions.ActionAdvancedInfo;
@@ -34,6 +37,9 @@ import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
public class ScoreReviewAction extends ProcessingAction {
private static final Logger log = LogManager.getLogger(ScoreReviewAction.class);
private final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
// Option(s)
public static final String SUBMIT_SCORE = "submit_score";
@@ -114,7 +120,14 @@ public class ScoreReviewAction extends ProcessingAction {
@Override
public List<String> getOptions() {
return List.of(SUBMIT_SCORE, RETURN_TO_POOL);
List<String> options = new ArrayList<>();
options.add(SUBMIT_SCORE);
if (configurationService.getBooleanProperty("workflow.reviewer.file-edit", false)) {
options.add(SUBMIT_EDIT_METADATA);
}
options.add(RETURN_TO_POOL);
return options;
}
@Override

8
dspace-api/src/main/java/org/dspace/xmlworkflow/state/actions/processingaction/SingleUserReviewAction.java
View File

@@ -21,6 +21,8 @@ import org.dspace.content.WorkspaceItem;
import org.dspace.content.factory.ContentServiceFactory;
import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.workflow.WorkflowException;
import org.dspace.xmlworkflow.factory.XmlWorkflowServiceFactory;
import org.dspace.xmlworkflow.state.Step;
@@ -40,6 +42,9 @@ import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
public class SingleUserReviewAction extends ProcessingAction {
private static final Logger log = LogManager.getLogger(SingleUserReviewAction.class);
private final ConfigurationService configurationService
= DSpaceServicesFactory.getInstance().getConfigurationService();
public static final int OUTCOME_REJECT = 1;
protected static final String SUBMIT_DECLINE_TASK = "submit_decline_task";
@@ -95,6 +100,9 @@ public class SingleUserReviewAction extends ProcessingAction {
public List<String> getOptions() {
List<String> options = new ArrayList<>();
options.add(SUBMIT_APPROVE);
if (configurationService.getBooleanProperty("workflow.reviewer.file-edit", false)) {
options.add(SUBMIT_EDIT_METADATA);
}
options.add(SUBMIT_REJECT);
options.add(SUBMIT_DECLINE_TASK);
return options;

16
dspace-api/src/main/java/org/dspace/xmlworkflow/storedcomponents/PoolTaskServiceImpl.java
View File

@@ -13,6 +13,7 @@ import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.collections4.CollectionUtils;
@@ -100,12 +101,17 @@ public class PoolTaskServiceImpl implements PoolTaskService {
//If the user does not have a claimedtask yet, see whether one of the groups of the user has pooltasks
//for this workflow item
Set<Group> groups = groupService.allMemberGroupsSet(context, ePerson);
for (Group group : groups) {
poolTask = poolTaskDAO.findByWorkflowItemAndGroup(context, group, workflowItem);
if (poolTask != null) {
return poolTask;
}
List<PoolTask> generalTasks = poolTaskDAO.findByWorkflowItem(context, workflowItem);
Optional<PoolTask> firstClaimedTask = groups.stream()
.flatMap(group -> generalTasks.stream()
.filter(f -> f.getGroup().getID().equals(group.getID()))
.findFirst()
.stream())
.findFirst();
if (firstClaimedTask.isPresent()) {
return firstClaimedTask.get();
}
}
}

21
dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/h2/V7.6_2024.12.17__workspaceitem_add_item_id_unique_constraint.sql Normal file
View File

@@ -0,0 +1,21 @@
--
-- The contents of this file are subject to the license and copyright
-- detailed in the LICENSE and NOTICE files at the root of the source
-- tree and available online at
--
-- http://www.dspace.org/license/
--
-- In the workspaceitem table, if there are multiple rows referring to the same item ID, keep only the first of them.
DELETE FROM workspaceitem WHERE EXISTS (
SELECT item_id
FROM workspaceitem
GROUP BY item_id
HAVING COUNT(workspace_item_id) > 1
) AND workspaceitem.workspace_item_id NOT IN (
SELECT MIN(workspace_item_id) AS workspace_item_id
FROM workspaceitem
GROUP BY item_id
);
-- Identify which rows have duplicates, and compute their replacements.
ALTER TABLE workspaceitem ADD CONSTRAINT unique_item_id UNIQUE(item_id);

21
dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/V7.6_2024.12.17__workspaceitem_add_item_id_unique_constraint.sql Normal file
View File

@@ -0,0 +1,21 @@
--
-- The contents of this file are subject to the license and copyright
-- detailed in the LICENSE and NOTICE files at the root of the source
-- tree and available online at
--
-- http://www.dspace.org/license/
--
-- In the workspaceitem table, if there are multiple rows referring to the same item ID, keep only the first of them.
WITH dedup AS (
SELECT item_id, MIN(workspace_item_id) AS workspace_item_id
FROM workspaceitem
GROUP BY item_id
HAVING COUNT(workspace_item_id) > 1
)
DELETE FROM workspaceitem
USING dedup
WHERE workspaceitem.item_id = dedup.item_id AND workspaceitem.workspace_item_id <> dedup.workspace_item_id;
-- Enforce uniqueness of item_id in workspaceitem table.
ALTER TABLE workspaceitem ADD CONSTRAINT unique_item_id UNIQUE(item_id);

10
dspace-api/src/test/data/dspaceFolder/config/controlled-vocabularies/countries.xml Normal file
View File

@@ -0,0 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<node id='Countries' label='Countries'>
<isComposedBy>
<node id='Africa' label='Africa'>
<isComposedBy>
<node id='DZA' label='Algeria'/>
</isComposedBy>
</node>
</isComposedBy>
</node>

10
dspace-api/src/test/data/dspaceFolder/config/controlled-vocabularies/countries_de.xml Normal file
View File

@@ -0,0 +1,10 @@
<?xml version="1.0" encoding="UTF-8"?>
<node id='Countries' label='Länder'>
<isComposedBy>
<node id='Africa' label='Afrika'>
<isComposedBy>
<node id='DZA' label='Algerien'/>
</isComposedBy>
</node>
</isComposedBy>
</node>

3
dspace-api/src/test/data/dspaceFolder/config/local.cfg
View File

@@ -175,6 +175,9 @@ authority.controlled.dspace.object.owner = true
webui.browse.link.1 = author:dc.contributor.*
webui.browse.link.2 = subject:dc.subject.*
# Configuration required for testing the controlled vocabulary functionality, which is configured using properties
vocabulary.plugin.countries.hierarchy.store=false
vocabulary.plugin.countries.storeIDs=true
# Enable duplicate detection for tests
duplicate.enable = true

24
dspace-api/src/test/java/org/dspace/AbstractDSpaceIntegrationTest.java
View File

@@ -21,8 +21,12 @@ import org.dspace.builder.AbstractBuilder;
import org.dspace.discovery.SearchUtils;
import org.dspace.servicemanager.DSpaceKernelImpl;
import org.dspace.servicemanager.DSpaceKernelInit;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Rule;
import org.junit.rules.TestName;
/**
* Abstract Test class copied from DSpace API
@@ -46,6 +50,12 @@ public class AbstractDSpaceIntegrationTest {
*/
protected static DSpaceKernelImpl kernelImpl;
/**
* Obtain the TestName from JUnit, so that we can print it out in the test logs (see below)
*/
@Rule
public TestName testName = new TestName();
/**
* Default constructor
*/
@@ -90,6 +100,20 @@ public class AbstractDSpaceIntegrationTest {
}
}
@Before
public void printTestMethodBefore() {
// Log the test method being executed. Put lines around it to make it stand out.
log.info("---");
log.info("Starting execution of test method: {}()", testName.getMethodName());
log.info("---");
}
@After
public void printTestMethodAfter() {
// Log the test method just completed.
log.info("Finished execution of test method: {}()", testName.getMethodName());
}
/**
* This method will be run after all tests finish as per @AfterClass. It
* will clean resources initialized by the @BeforeClass methods.

23
dspace-api/src/test/java/org/dspace/AbstractDSpaceTest.java
View File

@@ -18,9 +18,13 @@ import java.util.TimeZone;
import org.apache.logging.log4j.Logger;
import org.dspace.servicemanager.DSpaceKernelImpl;
import org.dspace.servicemanager.DSpaceKernelInit;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.rules.TestName;
import org.junit.runner.RunWith;
import org.mockito.junit.MockitoJUnitRunner;
@@ -62,6 +66,12 @@ public class AbstractDSpaceTest {
*/
protected static DSpaceKernelImpl kernelImpl;
/**
* Obtain the TestName from JUnit, so that we can print it out in the test logs (see below)
*/
@Rule
public TestName testName = new TestName();
/**
* This method will be run before the first test as per @BeforeClass. It will
* initialize shared resources required for all tests of this class.
@@ -94,6 +104,19 @@ public class AbstractDSpaceTest {
}
}
@Before
public void printTestMethodBefore() {
// Log the test method being executed. Put lines around it to make it stand out.
log.info("---");
log.info("Starting execution of test method: {}()", testName.getMethodName());
log.info("---");
}
@After
public void printTestMethodAfter() {
// Log the test method just completed.
log.info("Finished execution of test method: {}()", testName.getMethodName());
}
/**
* This method will be run after all tests finish as per @AfterClass. It

48
dspace-api/src/test/java/org/dspace/AbstractIntegrationTestWithDatabase.java
View File

@@ -20,8 +20,8 @@ import org.dspace.app.launcher.ScriptLauncher;
import org.dspace.app.scripts.handler.impl.TestDSpaceRunnableHandler;
import org.dspace.authority.AuthoritySearchService;
import org.dspace.authority.MockAuthoritySolrServiceImpl;
import org.dspace.authorize.AuthorizeException;
import org.dspace.builder.AbstractBuilder;
import org.dspace.builder.EPersonBuilder;
import org.dspace.content.Community;
import org.dspace.core.Context;
import org.dspace.core.I18nUtil;
@@ -127,19 +127,16 @@ public class AbstractIntegrationTestWithDatabase extends AbstractDSpaceIntegrati
EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
eperson = ePersonService.findByEmail(context, "test@email.com");
if (eperson == null) {
// This EPerson creation should only happen once (i.e. for first test run)
log.info("Creating initial EPerson (email=test@email.com) for Unit Tests");
eperson = ePersonService.create(context);
eperson.setFirstName(context, "first");
eperson.setLastName(context, "last");
eperson.setEmail("test@email.com");
eperson.setCanLogIn(true);
eperson.setLanguage(context, I18nUtil.getDefaultLocale().getLanguage());
ePersonService.setPassword(eperson, password);
// actually save the eperson to unit testing DB
ePersonService.update(context, eperson);
// Create test EPerson for usage in all tests
log.info("Creating Test EPerson (email=test@email.com) for Integration Tests");
eperson = EPersonBuilder.createEPerson(context)
.withNameInMetadata("first", "last")
.withEmail("test@email.com")
.withCanLogin(true)
.withLanguage(I18nUtil.getDefaultLocale().getLanguage())
.withPassword(password)
.build();
}
// Set our global test EPerson as the current user in DSpace
context.setCurrentUser(eperson);
@@ -148,26 +145,23 @@ public class AbstractIntegrationTestWithDatabase extends AbstractDSpaceIntegrati
admin = ePersonService.findByEmail(context, "admin@email.com");
if (admin == null) {
// This EPerson creation should only happen once (i.e. for first test run)
log.info("Creating initial EPerson (email=admin@email.com) for Unit Tests");
admin = ePersonService.create(context);
admin.setFirstName(context, "first (admin)");
admin.setLastName(context, "last (admin)");
admin.setEmail("admin@email.com");
admin.setCanLogIn(true);
admin.setLanguage(context, I18nUtil.getDefaultLocale().getLanguage());
ePersonService.setPassword(admin, password);
// actually save the eperson to unit testing DB
ePersonService.update(context, admin);
// Create test Administrator for usage in all tests
log.info("Creating Test Admin EPerson (email=admin@email.com) for Integration Tests");
admin = EPersonBuilder.createEPerson(context)
.withNameInMetadata("first (admin)", "last (admin)")
.withEmail("admin@email.com")
.withCanLogin(true)
.withLanguage(I18nUtil.getDefaultLocale().getLanguage())
.withPassword(password)
.build();
// Add Test Administrator to the ADMIN group in test database
GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
Group adminGroup = groupService.findByName(context, Group.ADMIN);
groupService.addMember(context, adminGroup, admin);
}
context.restoreAuthSystemState();
} catch (AuthorizeException ex) {
log.error("Error creating initial eperson or default groups", ex);
fail("Error creating initial eperson or default groups in AbstractUnitTest init()");
} catch (SQLException ex) {
log.error(ex.getMessage(), ex);
fail("SQL Error on AbstractUnitTest init()");

5
dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java
View File

@@ -23,7 +23,8 @@ import java.util.List;
import com.google.common.io.Files;
import com.opencsv.CSVReader;
import com.opencsv.exceptions.CsvException;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.app.launcher.ScriptLauncher;
import org.dspace.app.scripts.handler.impl.TestDSpaceRunnableHandler;
@@ -51,7 +52,7 @@ public class MetadataExportSearchIT extends AbstractIntegrationTestWithDatabase
private Item[] itemsSubject2 = new Item[numberItemsSubject2];
private String filename;
private Collection collection;
private Logger logger = Logger.getLogger(MetadataExportSearchIT.class);
private Logger logger = LogManager.getLogger(MetadataExportSearchIT.class);
private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
private SearchService searchService;

5
dspace-api/src/test/java/org/dspace/builder/OrcidHistoryBuilder.java
View File

@@ -11,7 +11,8 @@ import java.io.IOException;
import java.sql.SQLException;
import java.util.Date;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Item;
import org.dspace.core.Context;
import org.dspace.orcid.OrcidHistory;
@@ -24,7 +25,7 @@ import org.dspace.orcid.service.OrcidHistoryService;
*/
public class OrcidHistoryBuilder extends AbstractBuilder<OrcidHistory, OrcidHistoryService> {
private static final Logger log = Logger.getLogger(OrcidHistoryBuilder.class);
private static final Logger log = LogManager.getLogger(OrcidHistoryBuilder.class);
private OrcidHistory orcidHistory;

7
dspace-api/src/test/java/org/dspace/content/VersioningWithRelationshipsIT.java
View File

@@ -59,7 +59,7 @@ import org.dspace.content.virtual.Collected;
import org.dspace.content.virtual.VirtualMetadataConfiguration;
import org.dspace.content.virtual.VirtualMetadataPopulator;
import org.dspace.core.Constants;
import org.dspace.discovery.SolrSearchCore;
import org.dspace.discovery.MockSolrSearchCore;
import org.dspace.kernel.ServiceManager;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.dspace.versioning.Version;
@@ -79,8 +79,9 @@ public class VersioningWithRelationshipsIT extends AbstractIntegrationTestWithDa
ContentServiceFactory.getInstance().getInstallItemService();
private final ItemService itemService =
ContentServiceFactory.getInstance().getItemService();
private final SolrSearchCore solrSearchCore =
DSpaceServicesFactory.getInstance().getServiceManager().getServicesByType(SolrSearchCore.class).get(0);
private final MockSolrSearchCore solrSearchCore =
DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName(null, MockSolrSearchCore.class);
protected Community community;
protected Collection collection;
protected EntityType publicationEntityType;

12
dspace-api/src/test/java/org/dspace/content/WorkspaceItemTest.java
View File

@@ -12,6 +12,7 @@ import static org.hamcrest.CoreMatchers.notNullValue;
import static org.hamcrest.CoreMatchers.nullValue;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertThrows;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.any;
@@ -39,6 +40,7 @@ import org.dspace.core.Context;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.factory.EPersonServiceFactory;
import org.dspace.eperson.service.EPersonService;
import org.dspace.workflow.MockWorkflowItem;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -468,4 +470,14 @@ public class WorkspaceItemTest extends AbstractUnitTest {
assertTrue("testSetPublishedBefore 0", wi.isPublishedBefore());
}
@Test
public void testDuplicateItemID() throws Exception {
context.turnOffAuthorisationSystem();
Item item = wi.getItem();
MockWorkflowItem wfItem = new MockWorkflowItem();
wfItem.item = item;
wfItem.collection = collection;
assertThrows(IllegalArgumentException.class, () -> workspaceItemService.create(context, wfItem));
context.restoreAuthSystemState();
}
}

139
dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java
View File

@@ -89,6 +89,145 @@ public class DSpaceControlledVocabularyTest extends AbstractDSpaceTest {
assertEquals("north 40", result.values[0].value);
}
/**
* Test of getMatches method of class
* DSpaceControlledVocabulary using a localized controlled vocabulary with no locale (fallback to default)
* @throws java.lang.ClassNotFoundException passed through.
*/
@Test
public void testGetMatchesNoLocale() throws ClassNotFoundException {
final String PLUGIN_INTERFACE = "org.dspace.content.authority.ChoiceAuthority";
String idValue = "DZA";
String labelPart = "Alge";
int start = 0;
int limit = 10;
// This "countries" Controlled Vocab is included in TestEnvironment data
// (under /src/test/data/dspaceFolder/) and it should be auto-loaded
// by test configs in /src/test/data/dspaceFolder/config/local.cfg
DSpaceControlledVocabulary instance = (DSpaceControlledVocabulary)
CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE),
"countries");
assertNotNull(instance);
Choices result = instance.getMatches(labelPart, start, limit, null);
assertEquals(idValue, result.values[0].value);
assertEquals("Algeria", result.values[0].label);
}
/**
* Test of getBestMatch method of class
* DSpaceControlledVocabulary using a localized controlled vocabulary with no locale (fallback to default)
* @throws java.lang.ClassNotFoundException passed through.
*/
@Test
public void testGetBestMatchIdValueNoLocale() throws ClassNotFoundException {
final String PLUGIN_INTERFACE = "org.dspace.content.authority.ChoiceAuthority";
String idValue = "DZA";
// This "countries" Controlled Vocab is included in TestEnvironment data
// (under /src/test/data/dspaceFolder/) and it should be auto-loaded
// by test configs in /src/test/data/dspaceFolder/config/local.cfg
DSpaceControlledVocabulary instance = (DSpaceControlledVocabulary)
CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE),
"countries");
assertNotNull(instance);
Choices result = instance.getBestMatch(idValue, null);
assertEquals(idValue, result.values[0].value);
assertEquals("Algeria", result.values[0].label);
}
/**
* Test of getMatches method of class
* DSpaceControlledVocabulary using a localized controlled vocabulary with valid locale parameter (localized
* label returned)
*/
@Test
public void testGetMatchesGermanLocale() throws ClassNotFoundException {
final String PLUGIN_INTERFACE = "org.dspace.content.authority.ChoiceAuthority";
String idValue = "DZA";
String labelPart = "Alge";
int start = 0;
int limit = 10;
// This "countries" Controlled Vocab is included in TestEnvironment data
// (under /src/test/data/dspaceFolder/) and it should be auto-loaded
// by test configs in /src/test/data/dspaceFolder/config/local.cfg
DSpaceControlledVocabulary instance = (DSpaceControlledVocabulary)
CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE),
"countries");
assertNotNull(instance);
Choices result = instance.getMatches(labelPart, start, limit, "de");
assertEquals(idValue, result.values[0].value);
assertEquals("Algerien", result.values[0].label);
}
/**
* Test of getBestMatch method of class
* DSpaceControlledVocabulary using a localized controlled vocabulary with valid locale parameter (localized
* label returned)
*/
@Test
public void testGetBestMatchIdValueGermanLocale() throws ClassNotFoundException {
final String PLUGIN_INTERFACE = "org.dspace.content.authority.ChoiceAuthority";
String idValue = "DZA";
// This "countries" Controlled Vocab is included in TestEnvironment data
// (under /src/test/data/dspaceFolder/) and it should be auto-loaded
// by test configs in /src/test/data/dspaceFolder/config/local.cfg
DSpaceControlledVocabulary instance = (DSpaceControlledVocabulary)
CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE),
"countries");
assertNotNull(instance);
Choices result = instance.getBestMatch(idValue, "de");
assertEquals(idValue, result.values[0].value);
assertEquals("Algerien", result.values[0].label);
}
/**
* Test of getChoice method of class
* DSpaceControlledVocabulary using a localized controlled vocabulary with no locale (fallback to default)
* @throws java.lang.ClassNotFoundException passed through.
*/
@Test
public void testGetChoiceNoLocale() throws ClassNotFoundException {
final String PLUGIN_INTERFACE = "org.dspace.content.authority.ChoiceAuthority";
String idValue = "DZA";
// This "countries" Controlled Vocab is included in TestEnvironment data
// (under /src/test/data/dspaceFolder/) and it should be auto-loaded
// by test configs in /src/test/data/dspaceFolder/config/local.cfg
DSpaceControlledVocabulary instance = (DSpaceControlledVocabulary)
CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE),
"countries");
assertNotNull(instance);
Choice result = instance.getChoice(idValue, null);
assertEquals(idValue, result.value);
assertEquals("Algeria", result.label);
}
/**
* Test of getChoice method of class
* DSpaceControlledVocabulary using a localized controlled vocabulary with valid locale parameter (localized
* label returned)
* @throws java.lang.ClassNotFoundException passed through.
*/
@Test
public void testGetChoiceGermanLocale() throws ClassNotFoundException {
final String PLUGIN_INTERFACE = "org.dspace.content.authority.ChoiceAuthority";
String idValue = "DZA";
// This "countries" Controlled Vocab is included in TestEnvironment data
// (under /src/test/data/dspaceFolder/) and it should be auto-loaded
// by test configs in /src/test/data/dspaceFolder/config/local.cfg
DSpaceControlledVocabulary instance = (DSpaceControlledVocabulary)
CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE),
"countries");
assertNotNull(instance);
Choice result = instance.getChoice(idValue, "de");
assertEquals(idValue, result.value);
assertEquals("Algerien", result.label);
}
/**
* Test of getBestMatch method, of class DSpaceControlledVocabulary.
*/

25
dspace-api/src/test/java/org/dspace/core/ContextTest.java
View File

@@ -558,4 +558,29 @@ public class ContextTest extends AbstractUnitTest {
cleanupContext(instance);
}
@Test
public void testUncacheEntities() throws Throwable {
// To set up the test, ensure the cache contains more than the current user entity
groupService.findByName(context, Group.ANONYMOUS);
assertTrue("Cache size should be greater than one", context.getDBConnection().getCacheSize() > 1);
context.uncacheEntities();
assertThat("Cache size should be one (current user)", context.getDBConnection().getCacheSize(), equalTo(1L));
context.reloadEntity(context.getCurrentUser());
assertThat("Cache should only contain the current user", context.getDBConnection().getCacheSize(), equalTo(1L));
}
@Test
public void testUncacheEntity() throws Throwable {
// Remember the cache size after loading an entity
Group group = groupService.findByName(context, Group.ANONYMOUS);
long oldCacheSize = context.getDBConnection().getCacheSize();
// Uncache the entity
context.uncacheEntity(group);
long newCacheSize = context.getDBConnection().getCacheSize();
assertThat("Cache size should be reduced by one", newCacheSize, equalTo(oldCacheSize - 1));
}
}

22
dspace-api/src/test/java/org/dspace/core/HibernateDBConnectionTest.java
View File

@@ -205,6 +205,28 @@ public class HibernateDBConnectionTest extends AbstractUnitTest {
.contains(person));
}
/**
* Test of uncacheEntities method
*/
@Test
public void testUncacheEntities() throws SQLException {
// Get DBConnection associated with DSpace Context
HibernateDBConnection dbConnection = (HibernateDBConnection) context.getDBConnection();
EPerson person = context.getCurrentUser();
assertTrue("Current user should be cached in session", dbConnection.getSession()
.contains(person));
dbConnection.uncacheEntities();
assertFalse("Current user should be gone from cache", dbConnection.getSession()
.contains(person));
// Test ability to reload an uncached entity
person = dbConnection.reloadEntity(person);
assertTrue("Current user should be cached back in session", dbConnection.getSession()
.contains(person));
}
/**
* Test of uncacheEntity method
*/

61
dspace-api/src/test/java/org/dspace/ctask/general/CreateMissingIdentifiersIT.java
View File

@@ -10,10 +10,7 @@ package org.dspace.ctask.general;
import static org.junit.Assert.assertEquals;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.builder.CollectionBuilder;
import org.dspace.builder.CommunityBuilder;
import org.dspace.builder.ItemBuilder;
@@ -21,13 +18,11 @@ import org.dspace.content.Collection;
import org.dspace.content.Item;
import org.dspace.core.factory.CoreServiceFactory;
import org.dspace.curate.Curator;
import org.dspace.identifier.IdentifierProvider;
import org.dspace.identifier.IdentifierServiceImpl;
import org.dspace.identifier.AbstractIdentifierProviderIT;
import org.dspace.identifier.VersionedHandleIdentifierProvider;
import org.dspace.identifier.VersionedHandleIdentifierProviderWithCanonicalHandles;
import org.dspace.kernel.ServiceManager;
import org.dspace.services.ConfigurationService;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.junit.After;
import org.junit.Test;
/**
@@ -36,30 +31,19 @@ import org.junit.Test;
* @author mwood
*/
public class CreateMissingIdentifiersIT
extends AbstractIntegrationTestWithDatabase {
private ServiceManager serviceManager;
private IdentifierServiceImpl identifierService;
extends AbstractIdentifierProviderIT {
private static final String P_TASK_DEF
= "plugin.named.org.dspace.curate.CurationTask";
private static final String TASK_NAME = "test";
@Override
public void setUp() throws Exception {
super.setUp();
context.turnOffAuthorisationSystem();
serviceManager = DSpaceServicesFactory.getInstance().getServiceManager();
identifierService = serviceManager.getServicesByType(IdentifierServiceImpl.class).get(0);
// Clean out providers to avoid any being used for creation of community and collection
identifierService.setProviders(new ArrayList<>());
}
private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
@Test
public void testPerform()
throws IOException {
// Must remove any cached named plugins before creating a new one
CoreServiceFactory.getInstance().getPluginService().clearNamedPluginClasses();
ConfigurationService configurationService = kernelImpl.getConfigurationService();
// Define a new task dynamically
configurationService.setProperty(P_TASK_DEF,
CreateMissingIdentifiers.class.getCanonicalName() + " = " + TASK_NAME);
@@ -76,14 +60,7 @@ public class CreateMissingIdentifiersIT
.build();
/*
* Curate with regular test configuration -- should succeed.
*/
curator.curate(context, item);
int status = curator.getStatus(TASK_NAME);
assertEquals("Curation should succeed", Curator.CURATE_SUCCESS, status);
/*
* Now install an incompatible provider to make the task fail.
* First, install an incompatible provider to make the task fail.
*/
registerProvider(VersionedHandleIdentifierProviderWithCanonicalHandles.class);
@@ -92,22 +69,18 @@ public class CreateMissingIdentifiersIT
curator.getResult(TASK_NAME));
assertEquals("Curation should fail", Curator.CURATE_ERROR,
curator.getStatus(TASK_NAME));
}
@Override
@After
public void destroy() throws Exception {
super.destroy();
DSpaceServicesFactory.getInstance().getServiceManager().getApplicationContext().refresh();
}
// Unregister this non-default provider
unregisterProvider(VersionedHandleIdentifierProviderWithCanonicalHandles.class);
// Re-register the default provider (for later tests which may depend on it)
registerProvider(VersionedHandleIdentifierProvider.class);
private void registerProvider(Class type) {
// Register our new provider
serviceManager.registerServiceClass(type.getName(), type);
IdentifierProvider identifierProvider =
(IdentifierProvider) serviceManager.getServiceByName(type.getName(), type);
// Overwrite the identifier-service's providers with the new one to ensure only this provider is used
identifierService.setProviders(List.of(identifierProvider));
/*
* Now, verify curate with default Handle Provider works
* (and that our re-registration of the default provider above was successful)
*/
curator.curate(context, item);
int status = curator.getStatus(TASK_NAME);
assertEquals("Curation should succeed", Curator.CURATE_SUCCESS, status);
}
}

109
dspace-api/src/test/java/org/dspace/discovery/DiscoveryIT.java
View File

@@ -8,6 +8,10 @@
package org.dspace.discovery;
import static org.dspace.discovery.SolrServiceWorkspaceWorkflowRestrictionPlugin.DISCOVER_WORKSPACE_CONFIGURATION_NAME;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.hasItems;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
@@ -21,6 +25,10 @@ import java.util.List;
import java.util.stream.Collectors;
import jakarta.servlet.http.HttpServletRequest;
import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.SolrServerException;
import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrDocument;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.app.launcher.ScriptLauncher;
import org.dspace.app.scripts.handler.impl.TestDSpaceRunnableHandler;
@@ -99,6 +107,9 @@ public class DiscoveryIT extends AbstractIntegrationTestWithDatabase {
MetadataAuthorityService metadataAuthorityService = ContentAuthorityServiceFactory.getInstance()
.getMetadataAuthorityService();
MockSolrSearchCore solrSearchCore = DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName(null, MockSolrSearchCore.class);
@Override
@Before
public void setUp() throws Exception {
@@ -796,6 +807,104 @@ public class DiscoveryIT extends AbstractIntegrationTestWithDatabase {
}
}
/**
* Test designed to check if the submitter is not indexed in all in solr documents for items
* and the submitter authority is still indexed
* @throws SearchServiceException
*/
@Test
public void searchWithNoSubmitterTest() throws SearchServiceException {
configurationService.setProperty("discovery.index.item.submitter.enabled", false);
DiscoveryConfiguration defaultConf = SearchUtils.getDiscoveryConfiguration(context, "default", null);
// Populate the testing objects: create items in eperson's workspace and perform search in it
int numberItems = 10;
context.turnOffAuthorisationSystem();
EPerson submitter = null;
try {
submitter = EPersonBuilder.createEPerson(context).withEmail("submitter@example.org")
.withNameInMetadata("Peter", "Funny").build();
} catch (SQLException e) {
throw new RuntimeException(e);
}
context.setCurrentUser(submitter);
Community community = CommunityBuilder.createCommunity(context).build();
Collection collection = CollectionBuilder.createCollection(context, community).build();
for (int i = 0; i < numberItems; i++) {
ItemBuilder.createItem(context, collection)
.withTitle("item " + i)
.build();
}
context.restoreAuthSystemState();
// Build query with default parameters (except for workspaceConf)
QueryResponse result = null;
try {
result = solrSearchCore.getSolr().query(new SolrQuery(String.format(
"search.resourcetype:\"Item\"")));
} catch (SolrServerException e) {
throw new RuntimeException(e);
} catch (IOException e) {
throw new RuntimeException(e);
}
assertEquals(result.getResults().size(), numberItems);
for (SolrDocument doc : result.getResults()) {
assertThat(doc.getFieldNames(),
not(hasItems("submitter_keyword", "submitter_ac", "submitter_acid", "submitter_filter")));
assertThat(doc.getFieldNames(), hasItem("submitter_authority"));
}
}
/**
* Test designed to check if the submitter is indexed in all in solr documents for items
* @throws SearchServiceException
*/
@Test
public void searchWithSubmitterTest() throws SearchServiceException {
configurationService.setProperty("discovery.index.item.submitter.enabled", true);
DiscoveryConfiguration defaultConf = SearchUtils.getDiscoveryConfiguration(context, "default", null);
// Populate the testing objects: create items in eperson's workspace and perform search in it
int numberItems = 10;
context.turnOffAuthorisationSystem();
EPerson submitter = null;
try {
submitter = EPersonBuilder.createEPerson(context).withEmail("submitter@example.org")
.withNameInMetadata("Peter", "Funny").build();
} catch (SQLException e) {
throw new RuntimeException(e);
}
context.setCurrentUser(submitter);
Community community = CommunityBuilder.createCommunity(context).build();
Collection collection = CollectionBuilder.createCollection(context, community).build();
for (int i = 0; i < numberItems; i++) {
ItemBuilder.createItem(context, collection)
.withTitle("item " + i)
.build();
}
context.restoreAuthSystemState();
// Build query with default parameters (except for workspaceConf)
QueryResponse result = null;
try {
result = solrSearchCore.getSolr().query(new SolrQuery(String.format(
"search.resourcetype:\"Item\"")));
} catch (SolrServerException e) {
throw new RuntimeException(e);
} catch (IOException e) {
throw new RuntimeException(e);
}
assertEquals(result.getResults().size(), numberItems);
for (SolrDocument doc : result.getResults()) {
for (String fieldname : doc.getFieldNames()) {
assertThat(doc.getFieldNames(), hasItems("submitter_keyword","submitter_ac", "submitter_filter",
"submitter_authority"));
}
}
}
private void assertSearchQuery(String resourceType, int size) throws SearchServiceException {
assertSearchQuery(resourceType, size, size, 0, -1);
}

68
dspace-api/src/test/java/org/dspace/identifier/AbstractIdentifierProviderIT.java Normal file
View File

@@ -0,0 +1,68 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.identifier;
import java.util.ArrayList;
import java.util.List;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.kernel.ServiceManager;
import org.dspace.services.factory.DSpaceServicesFactory;
/**
* AbstractIdentifierProviderIT which contains a few useful utility methods for IdentifierProvider Integration Tests
*/
public class AbstractIdentifierProviderIT extends AbstractIntegrationTestWithDatabase {
protected final ServiceManager serviceManager = DSpaceServicesFactory.getInstance().getServiceManager();
protected final IdentifierServiceImpl identifierService =
serviceManager.getServicesByType(IdentifierServiceImpl.class).get(0);
/**
* Register a specific IdentifierProvider into the current IdentifierService (replacing any existing providers).
* This method will also ensure the IdentifierProvider service is registered in the DSpace Service Manager.
* @param type IdentifierProvider Class
*/
protected void registerProvider(Class type) {
// Register our new provider
IdentifierProvider identifierProvider =
(IdentifierProvider) DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName(type.getName(), type);
if (identifierProvider == null) {
DSpaceServicesFactory.getInstance().getServiceManager().registerServiceClass(type.getName(), type);
identifierProvider = (IdentifierProvider) DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName(type.getName(), type);
}
identifierService.setProviders(List.of(identifierProvider));
}
/**
* Unregister a specific IdentifierProvider from the current IdentifierService (removing all existing providers).
* This method will also ensure the IdentifierProvider service is unregistered in the DSpace Service Manager,
* which ensures it does not conflict with other IdentifierProvider services.
* @param type IdentifierProvider Class
*/
protected void unregisterProvider(Class type) {
// Find the provider service
IdentifierProvider identifierProvider =
(IdentifierProvider) DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName(type.getName(), type);
// If found, unregister it
if (identifierProvider == null) {
DSpaceServicesFactory.getInstance().getServiceManager().unregisterService(type.getName());
}
// Overwrite the identifier-service's providers with an empty list
identifierService.setProviders(new ArrayList<>());
}
}

49
dspace-api/src/test/java/org/dspace/identifier/VersionedHandleIdentifierProviderIT.java
View File

@@ -11,10 +11,7 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import org.dspace.AbstractIntegrationTestWithDatabase;
import org.dspace.authorize.AuthorizeException;
import org.dspace.builder.CollectionBuilder;
import org.dspace.builder.CommunityBuilder;
@@ -22,15 +19,10 @@ import org.dspace.builder.ItemBuilder;
import org.dspace.builder.VersionBuilder;
import org.dspace.content.Collection;
import org.dspace.content.Item;
import org.dspace.kernel.ServiceManager;
import org.dspace.services.factory.DSpaceServicesFactory;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
public class VersionedHandleIdentifierProviderIT extends AbstractIntegrationTestWithDatabase {
private ServiceManager serviceManager;
private IdentifierServiceImpl identifierService;
public class VersionedHandleIdentifierProviderIT extends AbstractIdentifierProviderIT {
private String firstHandle;
@@ -44,12 +36,6 @@ public class VersionedHandleIdentifierProviderIT extends AbstractIntegrationTest
public void setUp() throws Exception {
super.setUp();
context.turnOffAuthorisationSystem();
serviceManager = DSpaceServicesFactory.getInstance().getServiceManager();
identifierService = serviceManager.getServicesByType(IdentifierServiceImpl.class).get(0);
// Clean out providers to avoid any being used for creation of community and collection
identifierService.setProviders(new ArrayList<>());
parentCommunity = CommunityBuilder.createCommunity(context)
.withName("Parent Community")
.build();
@@ -58,33 +44,6 @@ public class VersionedHandleIdentifierProviderIT extends AbstractIntegrationTest
.build();
}
@After
@Override
public void destroy() throws Exception {
super.destroy();
// After this test has finished running, refresh application context and
// set the expected 'default' versioned handle provider back to ensure other tests don't fail
DSpaceServicesFactory.getInstance().getServiceManager().getApplicationContext().refresh();
}
private void registerProvider(Class type) {
// Register our new provider
IdentifierProvider identifierProvider =
(IdentifierProvider) DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName(type.getName(), type);
if (identifierProvider == null) {
DSpaceServicesFactory.getInstance().getServiceManager().registerServiceClass(type.getName(), type);
identifierProvider = (IdentifierProvider) DSpaceServicesFactory.getInstance().getServiceManager()
.getServiceByName(type.getName(), type);
}
// Overwrite the identifier-service's providers with the new one to ensure only this provider is used
identifierService = DSpaceServicesFactory.getInstance().getServiceManager()
.getServicesByType(IdentifierServiceImpl.class).get(0);
identifierService.setProviders(new ArrayList<>());
identifierService.setProviders(List.of(identifierProvider));
}
private void createVersions() throws SQLException, AuthorizeException {
itemV1 = ItemBuilder.createItem(context, collection)
.withTitle("First version")
@@ -96,7 +55,6 @@ public class VersionedHandleIdentifierProviderIT extends AbstractIntegrationTest
@Test
public void testDefaultVersionedHandleProvider() throws Exception {
registerProvider(VersionedHandleIdentifierProvider.class);
createVersions();
// Confirm the original item only has its original handle
@@ -125,6 +83,11 @@ public class VersionedHandleIdentifierProviderIT extends AbstractIntegrationTest
assertEquals(firstHandle, itemV3.getHandle());
assertEquals(2, itemV3.getHandles().size());
containsHandle(itemV3, firstHandle + ".3");
// Unregister this non-default provider
unregisterProvider(VersionedHandleIdentifierProviderWithCanonicalHandles.class);
// Re-register the default provider (for later tests)
registerProvider(VersionedHandleIdentifierProvider.class);
}
private void containsHandle(Item item, String handle) {

1
dspace-api/src/test/java/org/dspace/util/DSpaceKernelInitializer.java
View File

@@ -83,6 +83,7 @@ public class DSpaceKernelInitializer
* Initially look for JNDI Resource called "java:/comp/env/dspace.dir".
* If not found, use value provided in "dspace.dir" in Spring Environment
*/
@SuppressWarnings("BanJNDI")
private String getDSpaceHome(ConfigurableEnvironment environment) {
// Load the "dspace.dir" property from Spring's configuration.
// This gives us the location of our DSpace configuration, which is

62
dspace-api/src/test/java/org/dspace/workflow/MockWorkflowItem.java Normal file
View File

@@ -0,0 +1,62 @@
/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.workflow;
import org.dspace.content.Collection;
import org.dspace.content.Item;
import org.dspace.eperson.EPerson;
public class MockWorkflowItem implements WorkflowItem {
public Integer id;
public Item item;
public Collection collection;
public EPerson submitter;
boolean hasMultipleFiles;
boolean hasMultipleTitles;
boolean isPublishedBefore;
public Integer getID() {
return id;
}
public Item getItem() {
return item;
}
public Collection getCollection() {
return collection;
}
public EPerson getSubmitter() {
return submitter;
}
public boolean hasMultipleFiles() {
return hasMultipleFiles;
}
public void setMultipleFiles(boolean b) {
hasMultipleFiles = b;
}
public boolean hasMultipleTitles() {
return hasMultipleTitles;
}
public void setMultipleTitles(boolean b) {
hasMultipleTitles = b;
}
public boolean isPublishedBefore() {
return isPublishedBefore;
}
public void setPublishedBefore(boolean b) {
isPublishedBefore = b;
}
}

7
dspace-iiif/pom.xml
View File

@@ -44,6 +44,11 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</exclusion>
<!-- Spring JCL is unnecessary and conflicts with commons-logging when both are on classpath -->
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</exclusion>
</exclusions>
</dependency>
@@ -106,7 +111,7 @@
<dependency>
<groupId>de.digitalcollections.iiif</groupId>
<artifactId>iiif-apis</artifactId>
<version>0.3.10</version>
<version>0.3.11</version>
<exclusions>
<exclusion>
<groupId>org.javassist</groupId>

40
dspace-oai/pom.xml
View File

@@ -65,9 +65,8 @@
<!-- Java Injection -->
<dependency>
<groupId>javax.inject</groupId>
<artifactId>javax.inject</artifactId>
<version>1</version>
<groupId>jakarta.inject</groupId>
<artifactId>jakarta.inject-api</artifactId>
</dependency>
<!-- Needed to support Spring @Configuration classes (to register servlets/beans with Spring Boot webapp) -->
@@ -80,6 +79,11 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</exclusion>
<!-- Spring JCL is unnecessary and conflicts with commons-logging when both are on classpath -->
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</exclusion>
</exclusions>
</dependency>
@@ -94,22 +98,9 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</exclusion>
<!-- More recent version is pulled in via below dependencies -->
<exclusion>
<groupId>org.parboiled</groupId>
<artifactId>parboiled-java</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- Newer version, necessary to align with newer version of ASM in parent POM
This is needed by both jtwig-spring-boot-starter and our tests. -->
<dependency>
<groupId>org.parboiled</groupId>
<artifactId>parboiled-java</artifactId>
<version>1.3.1</version>
</dependency>
<!-- Internal -->
<dependency>
<groupId>org.dspace</groupId>
@@ -128,23 +119,6 @@
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-web</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j-impl</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
</dependency>
<!-- Testing -->
<dependency>

2
dspace-oai/src/main/java/org/dspace/xoai/app/CCElementItemCompilePlugin.java
View File

@@ -11,7 +11,7 @@ import java.util.List;
import com.lyncode.xoai.dataprovider.xml.xoai.Element;
import com.lyncode.xoai.dataprovider.xml.xoai.Metadata;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.StringUtils;
import org.dspace.content.Item;
import org.dspace.core.Context;
import org.dspace.license.factory.LicenseServiceFactory;

7
dspace-oai/src/main/java/org/dspace/xoai/app/XOAI.java
View File

@@ -9,7 +9,7 @@ package org.dspace.xoai.app;
import static com.lyncode.xoai.dataprovider.core.Granularity.Second;
import static java.util.Objects.nonNull;
import static org.apache.commons.lang.StringUtils.EMPTY;
import static org.apache.commons.lang3.StringUtils.EMPTY;
import static org.apache.solr.common.params.CursorMarkParams.CURSOR_MARK_PARAM;
import static org.apache.solr.common.params.CursorMarkParams.CURSOR_MARK_START;
import static org.dspace.xoai.util.ItemUtils.retrieveMetadata;
@@ -334,6 +334,11 @@ public class XOAI {
server.add(list);
server.commit();
list.clear();
try {
context.uncacheEntities();
} catch (SQLException ex) {
log.error("Error uncaching entities", ex);
}
}
}
System.out.println("Total: " + i + " items");

4
dspace-oai/src/main/java/org/dspace/xoai/filter/ItemsWithBitstreamFilter.java
View File

@@ -9,8 +9,8 @@ package org.dspace.xoai.filter;
import java.sql.SQLException;
import org.apache.log4j.LogManager;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.content.Bundle;
import org.dspace.content.Item;
import org.dspace.handle.factory.HandleServiceFactory;

7
dspace-oai/src/main/resources/static/style.xsl
View File

@@ -522,15 +522,14 @@
<xsl:choose>
<xsl:when test="normalize-space($path/../oai:resumptionToken/text()) = ''">
<!-- on the last page of results we have to assume that @completeListSize is available -->
<xsl:value-of
select="$total - $count" />
<xsl:value-of select="(number($total) - $count) + 1" />
-
<xsl:value-of select="$total" />
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="$cursor * $count" />
<xsl:value-of select="(number($cursor) * $count) + 1" />
-
<xsl:value-of select="($cursor+1) * $count" />
<xsl:value-of select="(number($cursor) + 1) * $count" />
</xsl:otherwise>
</xsl:choose>
</xsl:when>

9
dspace-oai/src/test/java/org/dspace/xoai/tests/integration/xoai/PipelineTest.java
View File

@@ -13,13 +13,14 @@ import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.MatcherAssert.assertThat;
import java.io.InputStream;
import java.nio.charset.Charset;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.stream.StreamSource;
import com.lyncode.xoai.util.XSLPipeline;
import org.apache.commons.io.IOUtils;
import org.dspace.xoai.tests.support.XmlMatcherBuilder;
import org.junit.Test;
import org.parboiled.common.FileUtils;
public class PipelineTest {
private static TransformerFactory factory = TransformerFactory.newInstance();
@@ -28,9 +29,9 @@ public class PipelineTest {
public void pipelineTest() throws Exception {
InputStream input = PipelineTest.class.getClassLoader().getResourceAsStream("item.xml");
InputStream xslt = PipelineTest.class.getClassLoader().getResourceAsStream("oai_dc.xsl");
String output = FileUtils.readAllText(new XSLPipeline(input, true)
.apply(factory.newTemplates(new StreamSource(xslt)))
.getTransformed());
String output = IOUtils.toString(new XSLPipeline(input, true)
.apply(factory.newTemplates(new StreamSource(xslt)))
.getTransformed(), Charset.defaultCharset());
assertThat(output, oai_dc().withXPath("/oai_dc:dc/dc:title", equalTo("Teste")));

13
dspace-rdf/pom.xml
View File

@@ -67,6 +67,11 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</exclusion>
<!-- Spring JCL is unnecessary and conflicts with commons-logging when both are on classpath -->
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</exclusion>
</exclusions>
</dependency>
@@ -80,14 +85,6 @@
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-web</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>

42
dspace-server-webapp/pom.xml
View File

@@ -31,7 +31,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.1.0</version>
<version>1.2.1</version>
<executions>
<execution>
<phase>initialize</phase>
@@ -293,14 +293,6 @@
<artifactId>spring-expression</artifactId>
<version>${spring.version}</version>
</dependency>
<!-- Specify the version of json-smart we want to use.
This solves a version mismatch between nimbus-jose-jwt and json-path below. -->
<!--<dependency>
<groupId>net.minidev</groupId>
<artifactId>json-smart</artifactId>
<version>2.5.0</version>
</dependency>-->
</dependencies>
</dependencyManagement>
@@ -343,6 +335,18 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
<version>${spring-boot.version}</version>
<exclusions>
<!-- Use version brought in by spring-boot-starter-web above -->
<exclusion>
<groupId>io.micrometer</groupId>
<artifactId>micrometer-observation</artifactId>
</exclusion>
<!-- Use version brought in by spring-boot-starter-web above -->
<exclusion>
<groupId>io.micrometer</groupId>
<artifactId>micrometer-commons</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
@@ -419,7 +423,7 @@
<dependency>
<groupId>org.webjars.npm</groupId>
<artifactId>json-editor__json-editor</artifactId>
<version>2.6.1</version>
<version>2.15.1</version>
</dependency>
<!-- Also pull in current version of Bootstrap via WebJars.
This is used by BOTH our HAL Browser and our OAI-PMH interface.
@@ -437,7 +441,7 @@
<artifactId>spring-boot-starter-security</artifactId>
<version>${spring-boot.version}</version>
<exclusions>
<!-- Later version brought in by spring-boot-starter-web above -->
<!-- Use version brought in by spring-boot-starter-web above -->
<exclusion>
<groupId>io.micrometer</groupId>
<artifactId>micrometer-observation</artifactId>
@@ -456,6 +460,11 @@
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</exclusion>
<!-- Spring JCL is unnecessary and conflicts with commons-logging when both are on classpath -->
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</exclusion>
</exclusions>
</dependency>
@@ -543,7 +552,7 @@
<dependency>
<groupId>net.minidev</groupId>
<artifactId>json-smart</artifactId>
<version>2.5.0</version>
<version>2.5.1</version>
</dependency>
<dependency>
@@ -581,7 +590,7 @@
<dependency>
<groupId>org.apache.httpcomponents.client5</groupId>
<artifactId>httpclient5</artifactId>
<version>5.3.1</version>
<version>5.4.1</version>
<scope>test</scope>
</dependency>
<dependency>
@@ -593,6 +602,13 @@
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
<exclusions>
<!-- We pull in a later version above -->
<exclusion>
<groupId>net.minidev</groupId>
<artifactId>json-smart</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>

2
dspace-server-webapp/src/main/java/org/dspace/app/rest/AuthenticationRestController.java
View File

@@ -220,7 +220,7 @@ public class AuthenticationRestController implements InitializingBean {
* @return ResponseEntity
*/
@RequestMapping(value = "/login", method = { RequestMethod.GET, RequestMethod.PUT, RequestMethod.PATCH,
RequestMethod.DELETE })
RequestMethod.DELETE })
public ResponseEntity login() {
return ResponseEntity.status(HttpStatus.METHOD_NOT_ALLOWED).body("Only POST is allowed for login requests.");
}

2
dspace-server-webapp/src/main/java/org/dspace/app/rest/ItemOwningCollectionUpdateRestController.java
View File

@@ -43,7 +43,7 @@ import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
/**
* This controller will handle all the incoming calls on the api/code/items/{uuid}/owningCollection endpoint
* This controller will handle all the incoming calls on the api/core/items/{uuid}/owningCollection endpoint
* where the uuid corresponds to the item of which you want to edit the owning collection.
*/
@RestController

173
dspace-server-webapp/src/main/java/org/dspace/app/rest/OpenSearchController.java
View File

@@ -7,11 +7,12 @@
*/
package org.dspace.app.rest;
import static org.dspace.app.rest.utils.HttpHeadersInitializer.CONTENT_DISPOSITION;
import static org.dspace.app.rest.utils.HttpHeadersInitializer.CONTENT_DISPOSITION_INLINE;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
@@ -21,10 +22,12 @@ import javax.xml.transform.stream.StreamResult;
import jakarta.servlet.ServletException;
import jakarta.servlet.http.HttpServletRequest;
import jakarta.servlet.http.HttpServletResponse;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.parameter.SearchFilter;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.app.rest.utils.RestDiscoverQueryBuilder;
import org.dspace.app.rest.utils.ScopeResolver;
import org.dspace.app.util.SyndicationFeed;
import org.dspace.app.util.factory.UtilServiceFactory;
import org.dspace.app.util.service.OpenSearchService;
import org.dspace.authorize.factory.AuthorizeServiceFactory;
@@ -49,6 +52,9 @@ import org.dspace.discovery.configuration.DiscoverySortConfiguration;
import org.dspace.discovery.configuration.DiscoverySortFieldConfiguration;
import org.dspace.discovery.indexobject.IndexableItem;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Sort;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.GetMapping;
@@ -86,22 +92,28 @@ public class OpenSearchController {
@Autowired
private ScopeResolver scopeResolver;
@Autowired
private RestDiscoverQueryBuilder restDiscoverQueryBuilder;
/**
* This method provides the OpenSearch query on the path /search
* It will pass the result as a OpenSearchDocument directly to the client
*/
@GetMapping("/search")
public void search(HttpServletRequest request,
HttpServletResponse response,
@RequestParam(name = "query", required = false) String query,
@RequestParam(name = "start", required = false) Integer start,
@RequestParam(name = "rpp", required = false) Integer count,
@RequestParam(name = "format", required = false) String format,
@RequestParam(name = "sort", required = false) String sort,
@RequestParam(name = "sort_direction", required = false) String sortDirection,
@RequestParam(name = "scope", required = false) String dsoObject,
Model model) throws IOException, ServletException {
HttpServletResponse response,
@RequestParam(name = "query", required = false) String query,
@RequestParam(name = "start", required = false) Integer start,
@RequestParam(name = "rpp", required = false) Integer count,
@RequestParam(name = "format", required = false) String format,
@RequestParam(name = "sort", required = false) String sort,
@RequestParam(name = "sort_direction", required = false) String sortDirection,
@RequestParam(name = "scope", required = false) String dsoObject,
@RequestParam(name = "configuration", required = false) String configuration,
List<SearchFilter> searchFilters,
Model model) throws IOException, ServletException {
context = ContextUtil.obtainContext(request);
if (start == null) {
start = 0;
}
@@ -133,84 +145,103 @@ public class OpenSearchController {
// then the rest - we are processing the query
IndexableObject container = null;
// support pagination parameters
DiscoverQuery queryArgs = new DiscoverQuery();
if (query == null) {
query = "";
} else {
queryArgs.setQuery(query);
DiscoverQuery queryArgs;
DiscoveryConfiguration discoveryConfiguration = null;
if (StringUtils.isNotBlank(configuration)) {
discoveryConfiguration = searchConfigurationService.getDiscoveryConfiguration(configuration);
}
queryArgs.setStart(start);
queryArgs.setMaxResults(count);
queryArgs.setDSpaceObjectFilter(IndexableItem.TYPE);
if (discoveryConfiguration == null) {
discoveryConfiguration = searchConfigurationService.getDiscoveryConfiguration("default");
}
// If we have search filters, use RestDiscoverQueryBuilder.
if (searchFilters != null && searchFilters.size() > 0) {
IndexableObject scope = scopeResolver.resolveScope(context, dsoObject);
Sort pageSort = sort == null || sortDirection == null
? Sort.unsorted()
: Sort.by(new Sort.Order(Sort.Direction.fromString(sortDirection), sort));
// TODO count can't be < 1 so I put an arbitrary number
Pageable page = PageRequest.of(start, count > 0 ? count : 10, pageSort);
queryArgs = restDiscoverQueryBuilder.buildQuery(context, scope,
discoveryConfiguration, query, searchFilters, IndexableItem.TYPE, page);
queryArgs.setFacetMinCount(-1);
} else { // Else, use the older behavior.
// support pagination parameters
queryArgs = new DiscoverQuery();
if (query == null) {
query = "";
} else {
queryArgs.setQuery(query);
}
queryArgs.setStart(start);
queryArgs.setMaxResults(count);
queryArgs.setDSpaceObjectFilter(IndexableItem.TYPE);
if (sort != null) {
DiscoveryConfiguration discoveryConfiguration =
searchConfigurationService.getDiscoveryConfiguration("");
if (discoveryConfiguration != null) {
DiscoverySortConfiguration searchSortConfiguration = discoveryConfiguration
.getSearchSortConfiguration();
if (searchSortConfiguration != null) {
DiscoverySortFieldConfiguration sortFieldConfiguration = searchSortConfiguration
.getSortFieldConfiguration(sort);
if (sortFieldConfiguration != null) {
String sortField = searchService
.toSortFieldIndex(sortFieldConfiguration.getMetadataField(),
sortFieldConfiguration.getType());
if (sort != null) {
if (discoveryConfiguration != null) {
DiscoverySortConfiguration searchSortConfiguration = discoveryConfiguration
.getSearchSortConfiguration();
if (searchSortConfiguration != null) {
DiscoverySortFieldConfiguration sortFieldConfiguration = searchSortConfiguration
.getSortFieldConfiguration(sort);
if (sortFieldConfiguration != null) {
String sortField = searchService
.toSortFieldIndex(sortFieldConfiguration.getMetadataField(),
sortFieldConfiguration.getType());
if (sortDirection != null && sortDirection.equals("DESC")) {
queryArgs.setSortField(sortField, SORT_ORDER.desc);
if (sortDirection != null && sortDirection.equals("DESC")) {
queryArgs.setSortField(sortField, SORT_ORDER.desc);
} else {
queryArgs.setSortField(sortField, SORT_ORDER.asc);
}
} else {
queryArgs.setSortField(sortField, SORT_ORDER.asc);
throw new IllegalArgumentException(sort + " is not a valid sort field");
}
} else {
throw new IllegalArgumentException(sort + " is not a valid sort field");
}
}
} else {
// this is the default sort so we want to switch this to date accessioned
queryArgs.setSortField("dc.date.accessioned_dt", SORT_ORDER.desc);
}
} else {
// this is the default sort so we want to switch this to date accessioned
queryArgs.setSortField("dc.date.accessioned_dt", SORT_ORDER.desc);
}
if (dsoObject != null) {
container = scopeResolver.resolveScope(context, dsoObject);
DiscoveryConfiguration discoveryConfiguration = searchConfigurationService
.getDiscoveryConfiguration(context, container);
queryArgs.setDiscoveryConfigurationName(discoveryConfiguration.getId());
queryArgs.addFilterQueries(discoveryConfiguration.getDefaultFilterQueries()
.toArray(
new String[discoveryConfiguration.getDefaultFilterQueries()
.size()]));
if (dsoObject != null) {
container = scopeResolver.resolveScope(context, dsoObject);
discoveryConfiguration = searchConfigurationService
.getDiscoveryConfigurationByNameOrIndexableObject(context, "site", container);
queryArgs.setDiscoveryConfigurationName(discoveryConfiguration.getId());
queryArgs.addFilterQueries(discoveryConfiguration.getDefaultFilterQueries()
.toArray(
new String[discoveryConfiguration.getDefaultFilterQueries()
.size()]));
}
}
// Perform the search
DiscoverResult qResults = null;
try {
qResults = SearchUtils.getSearchService().search(context,
container, queryArgs);
container, queryArgs);
} catch (SearchServiceException e) {
log.error(LogHelper.getHeader(context, "opensearch", "query="
+ queryArgs.getQuery()
+ ",error=" + e.getMessage()), e);
+ queryArgs.getQuery()
+ ",error=" + e.getMessage()), e);
throw new RuntimeException(e.getMessage(), e);
}
// Log
log.info("opensearch done, query=\"" + query + "\",results="
+ qResults.getTotalSearchResults());
+ qResults.getTotalSearchResults());
// format and return results
Map<String, String> labelMap = getLabels(request);
List<IndexableObject> dsoResults = qResults.getIndexableObjects();
Document resultsDoc = openSearchService.getResultsDoc(context, format, query,
(int) qResults.getTotalSearchResults(), qResults.getStart(),
qResults.getMaxResults(), container, dsoResults, labelMap);
(int) qResults.getTotalSearchResults(), qResults.getStart(),
qResults.getMaxResults(), container, dsoResults);
try {
Transformer xf = TransformerFactory.newInstance().newTransformer();
response.setContentType(openSearchService.getContentType(format));
response.addHeader(CONTENT_DISPOSITION, CONTENT_DISPOSITION_INLINE);
xf.transform(new DOMSource(resultsDoc),
new StreamResult(response.getWriter()));
new StreamResult(response.getWriter()));
} catch (TransformerException e) {
log.error(e);
throw new ServletException(e.toString());
@@ -231,7 +262,7 @@ public class OpenSearchController {
*/
@GetMapping("/service")
public void service(HttpServletRequest request,
HttpServletResponse response) throws IOException {
HttpServletResponse response) throws IOException {
log.debug("Show OpenSearch Service document");
if (openSearchService == null) {
openSearchService = UtilServiceFactory.getInstance().getOpenSearchService();
@@ -240,7 +271,7 @@ public class OpenSearchController {
String svcDescrip = openSearchService.getDescription(null);
log.debug("opensearchdescription is " + svcDescrip);
response.setContentType(openSearchService
.getContentType("opensearchdescription"));
.getContentType("opensearchdescription"));
response.setContentLength(svcDescrip.length());
response.getWriter().write(svcDescrip);
} else {
@@ -274,20 +305,4 @@ public class OpenSearchController {
public void setOpenSearchService(OpenSearchService oSS) {
openSearchService = oSS;
}
/**
* Internal method to get labels for the returned document
*/
private Map<String, String> getLabels(HttpServletRequest request) {
// TODO: get strings from translation file or configuration
Map<String, String> labelMap = new HashMap<String, String>();
labelMap.put(SyndicationFeed.MSG_UNTITLED, "notitle");
labelMap.put(SyndicationFeed.MSG_LOGO_TITLE, "logo.title");
labelMap.put(SyndicationFeed.MSG_FEED_DESCRIPTION, "general-feed.description");
for (String selector : SyndicationFeed.getDescriptionSelectors()) {
labelMap.put("metadata." + selector, selector);
}
return labelMap;
}
}

10
dspace-server-webapp/src/main/java/org/dspace/app/rest/UUIDLookupRestController.java
View File

@@ -24,9 +24,11 @@ import org.dspace.app.rest.model.DSpaceObjectRest;
import org.dspace.app.rest.utils.ContextUtil;
import org.dspace.app.rest.utils.DSpaceObjectUtils;
import org.dspace.app.rest.utils.Utils;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.service.AuthorizeService;
import org.dspace.content.DSpaceObject;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.discovery.SearchServiceException;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.hateoas.Link;
@@ -65,6 +67,9 @@ public class UUIDLookupRestController implements InitializingBean {
@Autowired
private DiscoverableEndpointsService discoverableEndpointsService;
@Autowired
private AuthorizeService authorizeService;
@Autowired
private ConverterService converter;
@@ -85,13 +90,14 @@ public class UUIDLookupRestController implements InitializingBean {
public void getDSObyIdentifier(HttpServletRequest request,
HttpServletResponse response,
@RequestParam(PARAM) UUID uuid)
throws IOException, SQLException, SearchServiceException {
throws IOException, SQLException, AuthorizeException {
Context context = null;
try {
context = ContextUtil.obtainContext(request);
DSpaceObject dso = dspaceObjectUtil.findDSpaceObject(context, uuid);
if (dso != null) {
authorizeService.authorizeAction(context, dso, Constants.READ);
DSpaceObjectRest dsor = converter.toRest(dso, utils.obtainProjection());
URI link = linkTo(dsor.getController(), dsor.getCategory(), dsor.getTypePlural()).slash(dsor.getId())
.toUri();

9
dspace-server-webapp/src/main/java/org/dspace/app/rest/converter/SearchEventConverter.java
View File

@@ -13,7 +13,8 @@ import java.util.LinkedList;
import java.util.List;
import jakarta.servlet.http.HttpServletRequest;
import org.apache.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.PageRest;
import org.dspace.app.rest.model.SearchEventRest;
import org.dspace.app.rest.model.SearchResultsRest;
@@ -31,7 +32,7 @@ import org.springframework.stereotype.Component;
@Component
public class SearchEventConverter {
/* Log4j logger */
private static final Logger log = Logger.getLogger(SearchEventConverter.class);
private static final Logger log = LogManager.getLogger(SearchEventConverter.class);
@Autowired
private ScopeResolver scopeResolver;
@@ -66,8 +67,8 @@ public class SearchEventConverter {
if (searchEventRest.getScope() != null) {
IndexableObject scopeObject =
scopeResolver.resolveScope(context, String.valueOf(searchEventRest.getScope()));
if (scopeObject instanceof DSpaceObject) {
usageSearchEvent.setScope((DSpaceObject) scopeObject);
if (scopeObject != null && scopeObject.getIndexedObject() instanceof DSpaceObject) {
usageSearchEvent.setScope((DSpaceObject) scopeObject.getIndexedObject());
}
}
usageSearchEvent.setConfiguration(searchEventRest.getConfiguration());

2
dspace-server-webapp/src/main/java/org/dspace/app/rest/converter/SubmissionSectionConverter.java
View File

@@ -10,6 +10,7 @@ package org.dspace.app.rest.converter;
import java.sql.SQLException;
import org.apache.logging.log4j.Logger;
import org.dspace.app.rest.model.ScopeEnum;
import org.dspace.app.rest.model.SubmissionSectionRest;
import org.dspace.app.rest.model.SubmissionVisibilityRest;
import org.dspace.app.rest.model.VisibilityEnum;
@@ -41,6 +42,7 @@ public class SubmissionSectionConverter implements DSpaceConverter<SubmissionSte
sp.setHeader(step.getHeading());
sp.setSectionType(step.getType());
sp.setId(step.getId());
sp.setScope(ScopeEnum.fromString(step.getScope()));
sp.setVisibility(new SubmissionVisibilityRest(VisibilityEnum.fromString(step.getVisibility()),
VisibilityEnum.fromString(step.getVisibilityOutside())));
return sp;

20
dspace-server-webapp/src/main/java/org/dspace/app/rest/converter/query/SearchQueryConverter.java
View File

@@ -7,6 +7,8 @@
*/
package org.dspace.app.rest.converter.query;
import static org.dspace.app.rest.model.SearchConfigurationRest.Filter.OPERATOR_QUERY;
import java.util.LinkedList;
import java.util.List;
@@ -16,23 +18,23 @@ import org.dspace.app.rest.model.query.RestSearchOperator;
import org.dspace.app.rest.parameter.SearchFilter;
/**
* This method will traverse a list of SearchFilters and transform any SearchFilters with an operator
* this is equal to 'Query' into a SearchFilter that has a standard DSpace operator like 'contains'
* Utility class for transforming a list of SearchFilters. Each SearchFilter with an operator set to 'query'
* is converted into a SearchFilter with a standard DSpace operator like 'contains'.
*/
public class SearchQueryConverter {
/**
* This method traverses the list of SearchFilters and transforms all of those that contain 'Query'
* This method traverses the list of SearchFilters and transforms all of those that with 'query'
* as the operator into a standard DSpace SearchFilter
*
* @param searchFilters The list of SearchFilters to be used
* @return A list of transformed SearchFilters
* @param searchFilters list of SearchFilters to be transformed
* @return list of transformed SearchFilters
*/
public List<SearchFilter> convert(List<SearchFilter> searchFilters) {
List<SearchFilter> transformedSearchFilters = new LinkedList<>();
for (SearchFilter searchFilter : CollectionUtils.emptyIfNull(searchFilters)) {
if (StringUtils.equals(searchFilter.getOperator(), "query")) {
if (StringUtils.equals(searchFilter.getOperator(), OPERATOR_QUERY)) {
SearchFilter transformedSearchFilter = convertQuerySearchFilterIntoStandardSearchFilter(searchFilter);
transformedSearchFilters.add(transformedSearchFilter);
} else {
@@ -46,10 +48,10 @@ public class SearchQueryConverter {
/**
* This method takes care of the converter of a specific SearchFilter given to it
*
* @param searchFilter The SearchFilter to be transformed
* @return The transformed SearchFilter
* @param searchFilter searchFilter to be transformed
* @return transformed SearchFilter
*/
public SearchFilter convertQuerySearchFilterIntoStandardSearchFilter(SearchFilter searchFilter) {
private SearchFilter convertQuerySearchFilterIntoStandardSearchFilter(SearchFilter searchFilter) {
RestSearchOperator restSearchOperator = RestSearchOperator.forQuery(searchFilter.getValue());
SearchFilter transformedSearchFilter = new SearchFilter(searchFilter.getName(),
restSearchOperator.getDspaceOperator(), restSearchOperator.extractValue(searchFilter.getValue()));

6
dspace-server-webapp/src/main/java/org/dspace/app/rest/model/AuthorizationRest.java
View File

@@ -18,9 +18,9 @@ import org.dspace.app.rest.RestResourceController;
* @author Andrea Bollini (andrea.bollini at 4science.it)
*/
@LinksRest(links = {
@LinkRest(method = "getEperson", name = AuthorizationRest.EPERSON),
@LinkRest(method = "getFeature", name = AuthorizationRest.FEATURE),
@LinkRest(method = "getObject", name = AuthorizationRest.OBJECT)
@LinkRest(method = "getEperson", name = AuthorizationRest.EPERSON),
@LinkRest(method = "getFeature", name = AuthorizationRest.FEATURE),
@LinkRest(method = "getObject", name = AuthorizationRest.OBJECT)
})
public class AuthorizationRest extends BaseObjectRest<String> {
public static final String NAME = "authorization";

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