MaDgiK-CITE
/
argos
13
0
Fork 0
Code Issues Pull Requests Projects Releases 3 Wiki Activity

Merge commit '8ca2b912d40ece8bf0fbcda5c49f1ef7f5f6fdfd'

This commit is contained in:
Diamantis Tziotzios 2020-04-02 13:33:08 +03:00
parent 1b4952a909 8ca2b912d4
commit 4ee39074a3
395 changed files with 17612 additions and 1854 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.gitignore vendored
View File

@ -38,3 +38,5 @@ dmp-frontend/.vscode/
dmp-frontend/package-lock.json
dmp-backend/logging/target/
ELK.Docker/shared/data-elk/

6
ELK.Docker/.env
View File

@ -1,3 +1,3 @@
TAG=6.3.1
ELASTIC_VERSION=6.3.1
ELASTIC_PASSWORD=changeme
ELK_VERSION=7.6.0
# Leave blank to use the "basic" image flavours, which include X-Pack.
# see https://www.elastic.co/subscriptions

2
ELK.Docker/.gitattributes vendored Normal file
View File

@ -0,0 +1,2 @@
# Declare files that will always have LF line endings on checkout.
*.sh text eol=lf

214
ELK.Docker/LICENSE
View File

@ -1,201 +1,21 @@
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
The MIT License (MIT)
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
Copyright (c) 2015 Anthony Lapenna
1. Definitions.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
"Licensor" shall mean the copyright owner or entity authorized by
the copyright owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.
"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.
"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or
Object form, made available under the License, as indicated by a
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.
2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
copyright license to reproduce, prepare Derivative Works of,
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.
3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:
(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and
(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and
(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and
(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.
You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.
9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason
of your accepting any such warranty or additional liability.
END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "{}"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright {yyyy} {name of copyright owner}
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

27
ELK.Docker/README.md
View File

@ -1,25 +1,4 @@
# stack-docker
This example Docker Compose configuration demonstrates many components of the
Elastic Stack, all running on a single machine under Docker.
Init default users and retrieve passwords
## Prerequisites
- Docker and Compose. Windows and Mac users get Compose installed automatically
with Docker. Linux users can:
```
pip install docker-compose
```
- At least 4GiB of RAM for the containers. Windows and Mac users _must_
configure their Docker virtual machine to have more than the default 2 GiB of
RAM:
![Docker VM memory settings](screenshots/docker-vm-memory-settings.png)
## Starting the stack
Try `docker-compose up` to create a demonstration Elastic Stack with
Elasticsearch, Kibana, Logstash, Auditbeat, Metricbeat, Filebeat, Packetbeat,
and Heartbeat.
Point a browser at [`http://localhost:5601`](http://localhost:5601) to see the results.
Log in with `elastic` / `changeme`.
1) connect to elasticsearch container with docker exec -it elastichsearch /bin/bash
2) run ./bin/elasticsearch-setup-passwords auto >./data/passwords.txt (press y and enter when the console shows nothing)

87
ELK.Docker/docker-compose.override.yml Normal file
View File

@ -0,0 +1,87 @@
version: '2.4'
services:
elasticsearch:
user: 1002:1002 #develuser
restart: unless-stopped
mem_limit: 2048m
environment:
- cluster.name=open-dmp-cluster
- bootstrap.memory_lock=true
- "ES_JAVA_OPTS=-Xmx1024m -Xms1024m"
- xpack.license.self_generated.type=basic
- xpack.monitoring.collection.enabled=true
- xpack.security.enabled=true
ulimits:
nproc: 65535
memlock:
soft: -1
hard: -1
volumes:
- ./shared/config-elk/elasticsearch/config/log4j2.properties:/usr/share/elasticsearch/config/log4j2.properties:ro
- ./shared/config-elk/elasticsearch/config/elasticsearch.yml:/usr/share/elasticsearch/config/elasticsearch.yml:ro
- ./shared/data-elk/elasticsearch-01-data:/usr/share/elasticsearch/data
- ./shared/data-elk/elasticsearch-01-log:/usr/share/elasticsearch/logs
#ports:
# - 51056:9200
# - 51057:9300
ports:
- "9200:9200"
expose:
- "9300"
networks:
open-dmp-elk-network:
logstash:
# user: 1002:1002 #develuser
volumes:
- ./shared/config-elk/logstash/config/logstash.yml:/usr/share/logstash/config/logstash.yml:ro
- ./shared/config-elk/logstash/config/pipelines.yml:/usr/share/logstash/config/pipelines.yml:ro
- ./shared/config-elk/logstash/config/log4j2.properties:/usr/share/logstash/config/log4j2.properties:ro
- ./shared/config-elk/logstash/pipeline:/usr/share/logstash/pipeline:ro
- ./shared/config-elk/logstash/logstash/templates:/usr/share/logstash/templates
- ./shared/data-elk/logstash-log:/usr/share/logstash/logs
- ./shared/data-elk/logstash-queue:/usr/share/logstash/queue
- ./shared/data-elk/logstash-dead_letter_queue:/usr/share/logstash/dead_letter_queue
expose:
- "31311"
- "31312"
restart: on-failure
mem_limit: 2048m
environment:
- LS_JAVA_OPTS=-Xmx1024m -Xms1024m
- xpack.license.self_generated.type=basic
- xpack.security.enabled=true
networks:
open-dmp-elk-network:
kibana:
# user: 1002:1002 #develuser
mem_limit: 512m
environment:
- xpack.license.self_generated.type=basic
- xpack.security.enabled=true
volumes:
- ./shared/config-elk/kibana/config:/usr/share/kibana/config:ro
#- ./shared/config-elk/kibana/certificates:/usr/share/kibana/certificates
restart: unless-stopped
ports:
- "51058:5601"
networks:
- open-dmp-elk-network
filebeat:
restart: unless-stopped
mem_limit: 256m
#command: [ "-e=false" ] # to overwrite the -e that disables logging to file!
volumes:
- ./shared/config-elk/filebeat/config/filebeat.yml:/usr/share/filebeat/filebeat.yml:ro
- ~/openDMP/logs:/usr/share/filebeat/log_data/dmp/
- ./shared/data-elk/filebeat-log:/usr/share/filebeat/logs
- ./shared/data-elk/filebeat-data:/usr/share/filebeat/data #For windows if we mount the data directory we get "Writing of registry returned error: sync /usr/share/filebeat/data/registry/filebeat: invalid argument."
networks:
- open-dmp-elk-network
networks:
open-dmp-elk-network:

200
ELK.Docker/docker-compose.yml
View File

@ -1,171 +1,43 @@
---
version: '3'
services:
# The environment variable "TAG" is used throughout this file to
# specify the version of the images to run. The default is set in the
# '.env' file in this folder. It can be overridden with any normal
# technique for setting environment variables, for example:
#
# TAG=6.0.0-beta1 docker-compose up
#
# REF: https://docs.docker.com/compose/compose-file/#variable-substitution
#
# Also be sure to set the ELASTIC_VERSION variable. For released versions,
# ${TAG} and ${ELASTIC_VERSION} will be identical, but for pre-release
# versions, ${TAG} might contain an extra build identifier, like
# "6.0.0-beta1-3eab5b40", so a full invocation might look like:
#
# ELASTIC_VERSION=6.0.0-beta1 TAG=6.0.0-beta1-3eab5b40 docker-compose up
#
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:${TAG}
container_name: elasticsearch
#volumes:
# - esdata:/usr/share/elasticsearch/data
environment: ['http.host=0.0.0.0', 'transport.host=127.0.0.1', 'ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
ports: ['0.0.0.0:9200:9200']
networks: ['stack']
version: '2.4'
kibana:
image: docker.elastic.co/kibana/kibana:${TAG}
container_name: kibana
ports: ['0.0.0.0:5601:5601']
networks: ['stack']
depends_on: ['elasticsearch']
services:
elasticsearch:
image: ${DOCKER_REGISTRY}elasticsearch
container_name: elasticsearch
build:
context: elasticsearch/
args:
ELK_VERSION: $ELK_VERSION
healthcheck:
# test: curl --cacert /usr/share/elasticsearch/config/certificates/ca/ca.crt -s https://localhost:9200 >/dev/null; if [[ $$? == 52 ]]; then echo 0; else echo 1; fi
interval: 30s
timeout: 10s
retries: 5
logstash:
image: docker.elastic.co/logstash/logstash:${TAG}
image: ${DOCKER_REGISTRY}logstash
container_name: logstash
# Provide a simple pipeline configuration for Logstash with a bind-mounted file.
volumes:
- ./config/logstash.conf:/usr/share/logstash/pipeline/logstash.conf
ports: ['0.0.0.0:31311:31311']
networks: ['stack']
depends_on: ['elasticsearch', 'setup_logstash']
build:
context: logstash/
args:
ELK_VERSION: $ELK_VERSION
depends_on:
- elasticsearch
kibana:
image: ${DOCKER_REGISTRY}kibana
build:
context: kibana/
args:
ELK_VERSION: $ELK_VERSION
depends_on:
- elasticsearch
filebeat:
image: docker.elastic.co/beats/filebeat:${TAG}
container_name: filebeat
command: -e -E 'output.elasticsearch.password=${ELASTIC_PASSWORD}'
# If the host system has logs at "/var/log", mount them at "/mnt/log"
# inside the container, where Filebeat can find them.
# volumes: ['/var/log:/mnt/log:ro']
networks: ['stack']
depends_on: ['elasticsearch', 'setup_filebeat']
heartbeat:
image: docker.elastic.co/beats/heartbeat:${TAG}
container_name: heartbeat
command: -e -E 'output.elasticsearch.password=${ELASTIC_PASSWORD}'
networks: ['stack']
depends_on: ['elasticsearch', 'setup_heartbeat']
# Run a short-lived container to set up Logstash.
setup_logstash:
image: centos:7
container_name: setup_logstash
volumes: ['./scripts/setup-logstash.sh:/usr/local/bin/setup-logstash.sh:ro']
# The script may have CR/LF line endings if using Docker for Windows, so
# make sure that they don't confuse Bash.
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-logstash.sh | tr -d "\r" | bash']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['elasticsearch']
setup_kibana:
image: centos:7
container_name: setup_kibana
volumes: ['./scripts/setup-kibana.sh:/usr/local/bin/setup-kibana.sh:ro']
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-kibana.sh | tr -d "\r" | bash']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['elasticsearch']
setup_filebeat:
image: docker.elastic.co/beats/filebeat:${TAG}
container_name: setup_filebeat
volumes: ['./scripts/setup-beat.sh:/usr/local/bin/setup-beat.sh:ro']
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-beat.sh | tr -d "\r" | bash -s filebeat']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['kibana']
setup_heartbeat:
image: docker.elastic.co/beats/heartbeat:${TAG}
container_name: setup_heartbeat
volumes: ['./scripts/setup-beat.sh:/usr/local/bin/setup-beat.sh:ro']
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-beat.sh | tr -d "\r" | bash -s heartbeat']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['kibana']
##########################DOCSBOX######################################################################
web:
restart: always
build: ./docsbox-master/docsbox
expose:
- "8000"
links:
- redis:redis
volumes:
- docsbox:/home/docsbox
- media:/home/docsbox/media
command: gunicorn -b :8000 docsbox:app
networks: ['stack']
rqworker:
restart: always
build: ./docsbox-master/docsbox
links:
- redis:redis
volumes:
- web
command: rq worker -c docsbox.settings
networks: ['stack']
rqscheduler:
restart: always
build: ./docsbox-master/docsbox
links:
- redis:redis
volumes:
- web
command: rqscheduler -H redis -p 6379 -d 0
networks: ['stack']
nginx:
restart: always
build: ./docsbox-master/nginx/
ports:
- "81:80"
volumes:
- web
links:
- web:web
networks: ['stack']
redis:
restart: always
image: redis:latest
expose:
- "6379"
volumes:
- redisdata:/data
networks: ['stack']
##########################SETTIGNS######################################################################
volumes:
#esdata:
#driver: local
redisdata:
driver: local
docsbox:
driver: local
media:
driver: local
networks: {stack: {}}
image: ${DOCKER_REGISTRY}filebeat
build:
context: filebeat/
args:
ELK_VERSION: $ELK_VERSION
depends_on:
- logstash

22
ELK.Docker/elasticsearch/Dockerfile Normal file
View File

@ -0,0 +1,22 @@
ARG ELK_VERSION
# https://github.com/elastic/elasticsearch-docker
FROM docker.elastic.co/elasticsearch/elasticsearch:${ELK_VERSION}
RUN /usr/share/elasticsearch/bin/elasticsearch-plugin install analysis-icu && \
/usr/share/elasticsearch/bin/elasticsearch-plugin install analysis-phonetic
RUN groupmod -g 1002 elasticsearch
RUN usermod -u 1002 -g 1002 elasticsearch
RUN chown -R elasticsearch /usr/share/elasticsearch
RUN sed -i -e 's/--userspec=1000/--userspec=1002/g' \
-e 's/UID 1000/UID 1002/' \
-e 's/chown -R 1000/chown -R 1002/' /usr/local/bin/docker-entrypoint.sh
RUN chown elasticsearch /usr/local/bin/docker-entrypoint.sh
ENV JAVA_HOME /usr/share/elasticsearch/jdk
# RUN mkdir /usr/share/elasticsearch/custom-plugins
# COPY plugins/elasticsearch-analysis-greeklish-7.5.1.zip /usr/share/elasticsearch/custom-plugins/elasticsearch-analysis-greeklish-7.5.1.zip
# RUN /usr/share/elasticsearch/bin/elasticsearch-plugin install file:///usr/share/elasticsearch/custom-plugins/elasticsearch-analysis-greeklish-7.5.1.zip

15
ELK.Docker/filebeat/Dockerfile Normal file
View File

@ -0,0 +1,15 @@
ARG ELK_VERSION
FROM docker.elastic.co/beats/filebeat:${ELK_VERSION}
# USER root
# RUN groupmod -g 1002 filebeat
# RUN usermod -u 1002 -g 1002 filebeat
# RUN chown -R filebeat /usr/share/filebeat
# RUN sed -i -e 's/--userspec=1000/--userspec=1002/g' \
# -e 's/UID 1000/UID 1002/' \
# -e 's/chown -R 1000/chown -R 1002/' /usr/local/bin/docker-entrypoint
# RUN chown filebeat /usr/local/bin/docker-entrypoint
# USER 1002:1002

15
ELK.Docker/kibana/Dockerfile Normal file
View File

@ -0,0 +1,15 @@
ARG ELK_VERSION
# https://github.com/elastic/kibana-docker
FROM docker.elastic.co/kibana/kibana:${ELK_VERSION}
# USER root
# RUN groupmod -g 1002 kibana
# RUN usermod -g 1002 root
# RUN usermod -u 1002 -g 1002 kibana
# RUN chown -R kibana /usr/share/kibana
# USER 1002:1002
# Add your kibana plugins setup here
# Example: RUN kibana-plugin install <name|url>

20
ELK.Docker/logstash/Dockerfile Normal file
View File

@ -0,0 +1,20 @@
ARG ELK_VERSION
# https://github.com/elastic/logstash-docker
FROM docker.elastic.co/logstash/logstash:${ELK_VERSION}
# USER root
# RUN groupmod -g 1002 logstash
# RUN usermod -u 1002 -g 1002 logstash
# RUN chown -R logstash /usr/share/logstash
# RUN sed -i -e 's/--userspec=1000/--userspec=1002/g' \
# -e 's/UID 1000/UID 1002/' \
# -e 's/chown -R 1000/chown -R 1002/' /usr/local/bin/docker-entrypoint
# RUN chown logstash /usr/local/bin/docker-entrypoint
# USER 1002:1002
# Add your logstash plugins setup here
# Example: RUN logstash-plugin install logstash-filter-json
RUN logstash-plugin update logstash-input-beats
RUN logstash-plugin update logstash-filter-grok

3
ELK.Docker/old/.env Normal file
View File

@ -0,0 +1,3 @@
TAG=6.3.1
ELASTIC_VERSION=6.3.1
ELASTIC_PASSWORD=changeme

0
ELK.Docker/.gitignore → ELK.Docker/old/.gitignore vendored
View File

0
ELK.Docker/.travis.yml → ELK.Docker/old/.travis.yml
View File

201
ELK.Docker/old/LICENSE Normal file
View File

@ -0,0 +1,201 @@
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.
"Licensor" shall mean the copyright owner or entity authorized by
the copyright owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.
"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.
"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or
Object form, made available under the License, as indicated by a
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.
2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
copyright license to reproduce, prepare Derivative Works of,
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.
3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:
(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and
(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and
(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and
(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.
You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.
9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason
of your accepting any such warranty or additional liability.
END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "{}"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright {yyyy} {name of copyright owner}
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

0
ELK.Docker/Makefile → ELK.Docker/old/Makefile
View File

25
ELK.Docker/old/README.md Normal file
View File

@ -0,0 +1,25 @@
# stack-docker
This example Docker Compose configuration demonstrates many components of the
Elastic Stack, all running on a single machine under Docker.
## Prerequisites
- Docker and Compose. Windows and Mac users get Compose installed automatically
with Docker. Linux users can:
```
pip install docker-compose
```
- At least 4GiB of RAM for the containers. Windows and Mac users _must_
configure their Docker virtual machine to have more than the default 2 GiB of
RAM:
![Docker VM memory settings](screenshots/docker-vm-memory-settings.png)
## Starting the stack
Try `docker-compose up` to create a demonstration Elastic Stack with
Elasticsearch, Kibana, Logstash, Auditbeat, Metricbeat, Filebeat, Packetbeat,
and Heartbeat.
Point a browser at [`http://localhost:5601`](http://localhost:5601) to see the results.
Log in with `elastic` / `changeme`.

0
ELK.Docker/config/logstash.conf → ELK.Docker/old/config/logstash.conf
View File

171
ELK.Docker/old/docker-compose.yml Normal file
View File

@ -0,0 +1,171 @@
---
version: '3'
services:
# The environment variable "TAG" is used throughout this file to
# specify the version of the images to run. The default is set in the
# '.env' file in this folder. It can be overridden with any normal
# technique for setting environment variables, for example:
#
# TAG=6.0.0-beta1 docker-compose up
#
# REF: https://docs.docker.com/compose/compose-file/#variable-substitution
#
# Also be sure to set the ELASTIC_VERSION variable. For released versions,
# ${TAG} and ${ELASTIC_VERSION} will be identical, but for pre-release
# versions, ${TAG} might contain an extra build identifier, like
# "6.0.0-beta1-3eab5b40", so a full invocation might look like:
#
# ELASTIC_VERSION=6.0.0-beta1 TAG=6.0.0-beta1-3eab5b40 docker-compose up
#
elasticsearch:
image: docker.elastic.co/elasticsearch/elasticsearch:${TAG}
container_name: elasticsearch
#volumes:
# - esdata:/usr/share/elasticsearch/data
environment: ['http.host=0.0.0.0', 'transport.host=127.0.0.1', 'ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
ports: ['0.0.0.0:9200:9200']
networks: ['stack']
kibana:
image: docker.elastic.co/kibana/kibana:${TAG}
container_name: kibana
ports: ['0.0.0.0:5601:5601']
networks: ['stack']
depends_on: ['elasticsearch']
logstash:
image: docker.elastic.co/logstash/logstash:${TAG}
container_name: logstash
# Provide a simple pipeline configuration for Logstash with a bind-mounted file.
volumes:
- ./config/logstash.conf:/usr/share/logstash/pipeline/logstash.conf
ports: ['0.0.0.0:31311:31311']
networks: ['stack']
depends_on: ['elasticsearch', 'setup_logstash']
filebeat:
image: docker.elastic.co/beats/filebeat:${TAG}
container_name: filebeat
command: -e -E 'output.elasticsearch.password=${ELASTIC_PASSWORD}'
# If the host system has logs at "/var/log", mount them at "/mnt/log"
# inside the container, where Filebeat can find them.
# volumes: ['/var/log:/mnt/log:ro']
networks: ['stack']
depends_on: ['elasticsearch', 'setup_filebeat']
heartbeat:
image: docker.elastic.co/beats/heartbeat:${TAG}
container_name: heartbeat
command: -e -E 'output.elasticsearch.password=${ELASTIC_PASSWORD}'
networks: ['stack']
depends_on: ['elasticsearch', 'setup_heartbeat']
# Run a short-lived container to set up Logstash.
setup_logstash:
image: centos:7
container_name: setup_logstash
volumes: ['./scripts/setup-logstash.sh:/usr/local/bin/setup-logstash.sh:ro']
# The script may have CR/LF line endings if using Docker for Windows, so
# make sure that they don't confuse Bash.
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-logstash.sh | tr -d "\r" | bash']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['elasticsearch']
setup_kibana:
image: centos:7
container_name: setup_kibana
volumes: ['./scripts/setup-kibana.sh:/usr/local/bin/setup-kibana.sh:ro']
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-kibana.sh | tr -d "\r" | bash']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['elasticsearch']
setup_filebeat:
image: docker.elastic.co/beats/filebeat:${TAG}
container_name: setup_filebeat
volumes: ['./scripts/setup-beat.sh:/usr/local/bin/setup-beat.sh:ro']
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-beat.sh | tr -d "\r" | bash -s filebeat']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['kibana']
setup_heartbeat:
image: docker.elastic.co/beats/heartbeat:${TAG}
container_name: setup_heartbeat
volumes: ['./scripts/setup-beat.sh:/usr/local/bin/setup-beat.sh:ro']
command: ['/bin/bash', '-c', 'cat /usr/local/bin/setup-beat.sh | tr -d "\r" | bash -s heartbeat']
environment: ['ELASTIC_PASSWORD=${ELASTIC_PASSWORD}']
networks: ['stack']
depends_on: ['kibana']
##########################DOCSBOX######################################################################
# web:
# restart: always
# build: ./docsbox-master/docsbox
# expose:
# - "8000"
# links:
# - redis:redis
# volumes:
# - docsbox:/home/docsbox
# - media:/home/docsbox/media
# command: gunicorn -b :8000 docsbox:app
# networks: ['stack']
#
# rqworker:
# restart: always
# build: ./docsbox-master/docsbox
# links:
# - redis:redis
# volumes:
# - web
# command: rq worker -c docsbox.settings
# networks: ['stack']
#
# rqscheduler:
# restart: always
# build: ./docsbox-master/docsbox
# links:
# - redis:redis
# volumes:
# - web
# command: rqscheduler -H redis -p 6379 -d 0
# networks: ['stack']
#
# nginx:
# restart: always
# build: ./docsbox-master/nginx/
# ports:
# - "81:80"
# volumes:
# - web
# links:
# - web:web
# networks: ['stack']
#
# redis:
# restart: always
# image: redis:latest
# expose:
# - "6379"
# volumes:
# - redisdata:/data
# networks: ['stack']
##########################SETTIGNS######################################################################
volumes:
#esdata:
#driver: local
redisdata:
driver: local
docsbox:
driver: local
media:
driver: local
networks: {stack: {}}

0
ELK.Docker/screenshots/docker-vm-memory-settings.png → ELK.Docker/old/screenshots/docker-vm-memory-settings.png
View File

Side by Side Swipe Overlay

Before

Width:  |  Height:  |  Size: 46 KiB

After

Width:  |  Height:  |  Size: 46 KiB

0
ELK.Docker/scripts/setup-beat.sh → ELK.Docker/old/scripts/setup-beat.sh
View File

0
ELK.Docker/scripts/setup-kibana.sh → ELK.Docker/old/scripts/setup-kibana.sh
View File

0
ELK.Docker/scripts/setup-logstash.sh → ELK.Docker/old/scripts/setup-logstash.sh
View File

0
ELK.Docker/stack/.gitignore → ELK.Docker/old/stack/.gitignore vendored
View File

20
ELK.Docker/shared/config-elk/elasticsearch/config/elasticsearch.yml Normal file
View File

@ -0,0 +1,20 @@
---
## Default Elasticsearch configuration from elasticsearch-docker.
## from https://github.com/elastic/elasticsearch-docker/blob/master/build/elasticsearch/elasticsearch.yml
#
network.host: 0.0.0.0
# minimum_master_nodes need to be explicitly set when bound on a public IP
# set to 1 to allow single node clusters
# Details: https://github.com/elastic/elasticsearch/pull/17288
# discovery.zen.minimum_master_nodes: 1
## Use single node discovery in order to disable production mode and avoid bootstrap checks
## see https://www.elastic.co/guide/en/elasticsearch/reference/current/bootstrap-checks.html
#
discovery.type: single-node
## Search Guard
#
cluster.routing.allocation.disk.watermark.flood_stage: 99%

179
ELK.Docker/shared/config-elk/elasticsearch/config/log4j2.properties Normal file
View File

@ -0,0 +1,179 @@
#https://github.com/elastic/elasticsearch/blob/7.4/distribution/src/config/log4j2.properties
status = error
# log action execution errors for easier debugging
logger.action.name = org.elasticsearch.action
logger.action.level = debug
appender.console.type = Console
appender.console.name = console
appender.console.layout.type = PatternLayout
appender.console.layout.pattern = [%d{ISO8601}][%-5p][%-25c{1.}] [%node_name]%marker %m%n
######## Server JSON ############################
appender.rolling.type = RollingFile
appender.rolling.name = rolling
appender.rolling.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}_server.json
appender.rolling.layout.type = ESJsonLayout
appender.rolling.layout.type_name = server
appender.rolling.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}-%d{yyyy-MM-dd}-%i.json.gz
appender.rolling.policies.type = Policies
appender.rolling.policies.time.type = TimeBasedTriggeringPolicy
appender.rolling.policies.time.interval = 1
appender.rolling.policies.time.modulate = true
appender.rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.rolling.policies.size.size = 128MB
appender.rolling.strategy.type = DefaultRolloverStrategy
appender.rolling.strategy.fileIndex = nomax
appender.rolling.strategy.action.type = Delete
appender.rolling.strategy.action.basepath = ${sys:es.logs.base_path}
appender.rolling.strategy.action.condition.type = IfFileName
appender.rolling.strategy.action.condition.glob = ${sys:es.logs.cluster_name}-*
appender.rolling.strategy.action.condition.nested_condition.type = IfAccumulatedFileSize
appender.rolling.strategy.action.condition.nested_condition.exceeds = 2GB
################################################
######## Server - old style pattern ###########
appender.rolling_old.type = RollingFile
appender.rolling_old.name = rolling_old
appender.rolling_old.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}.log
appender.rolling_old.layout.type = PatternLayout
appender.rolling_old.layout.pattern = [%d{ISO8601}][%-5p][%-25c{1.}] [%node_name]%marker %m%n
appender.rolling_old.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}-%d{yyyy-MM-dd}-%i.log.gz
appender.rolling_old.policies.type = Policies
appender.rolling_old.policies.time.type = TimeBasedTriggeringPolicy
appender.rolling_old.policies.time.interval = 1
appender.rolling_old.policies.time.modulate = true
appender.rolling_old.policies.size.type = SizeBasedTriggeringPolicy
appender.rolling_old.policies.size.size = 128MB
appender.rolling_old.strategy.type = DefaultRolloverStrategy
appender.rolling_old.strategy.fileIndex = nomax
appender.rolling_old.strategy.action.type = Delete
appender.rolling_old.strategy.action.basepath = ${sys:es.logs.base_path}
appender.rolling_old.strategy.action.condition.type = IfFileName
appender.rolling_old.strategy.action.condition.glob = ${sys:es.logs.cluster_name}-*
appender.rolling_old.strategy.action.condition.nested_condition.type = IfAccumulatedFileSize
appender.rolling_old.strategy.action.condition.nested_condition.exceeds = 2GB
################################################
rootLogger.level = info
rootLogger.appenderRef.console.ref = console
rootLogger.appenderRef.rolling.ref = rolling
rootLogger.appenderRef.rolling_old.ref = rolling_old
######## Deprecation JSON #######################
appender.deprecation_rolling.type = RollingFile
appender.deprecation_rolling.name = deprecation_rolling
appender.deprecation_rolling.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}_deprecation.json
appender.deprecation_rolling.layout.type = ESJsonLayout
appender.deprecation_rolling.layout.type_name = deprecation
appender.deprecation_rolling.layout.esmessagefields=x-opaque-id
appender.deprecation_rolling.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}_deprecation-%i.json.gz
appender.deprecation_rolling.policies.type = Policies
appender.deprecation_rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.deprecation_rolling.policies.size.size = 1GB
appender.deprecation_rolling.strategy.type = DefaultRolloverStrategy
appender.deprecation_rolling.strategy.max = 4
#################################################
######## Deprecation - old style pattern #######
appender.deprecation_rolling_old.type = RollingFile
appender.deprecation_rolling_old.name = deprecation_rolling_old
appender.deprecation_rolling_old.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}_deprecation.log
appender.deprecation_rolling_old.layout.type = PatternLayout
appender.deprecation_rolling_old.layout.pattern = [%d{ISO8601}][%-5p][%-25c{1.}] [%node_name]%marker %m%n
appender.deprecation_rolling_old.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}\
_deprecation-%i.log.gz
appender.deprecation_rolling_old.policies.type = Policies
appender.deprecation_rolling_old.policies.size.type = SizeBasedTriggeringPolicy
appender.deprecation_rolling_old.policies.size.size = 1GB
appender.deprecation_rolling_old.strategy.type = DefaultRolloverStrategy
appender.deprecation_rolling_old.strategy.max = 4
#################################################
logger.deprecation.name = org.elasticsearch.deprecation
logger.deprecation.level = warn
logger.deprecation.appenderRef.deprecation_rolling.ref = deprecation_rolling
logger.deprecation.appenderRef.deprecation_rolling_old.ref = deprecation_rolling_old
logger.deprecation.additivity = false
######## Search slowlog JSON ####################
appender.index_search_slowlog_rolling.type = RollingFile
appender.index_search_slowlog_rolling.name = index_search_slowlog_rolling
appender.index_search_slowlog_rolling.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs\
.cluster_name}_index_search_slowlog.json
appender.index_search_slowlog_rolling.layout.type = ESJsonLayout
appender.index_search_slowlog_rolling.layout.type_name = index_search_slowlog
appender.index_search_slowlog_rolling.layout.esmessagefields=message,took,took_millis,total_hits,types,stats,search_type,total_shards,source,id
appender.index_search_slowlog_rolling.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs\
.cluster_name}_index_search_slowlog-%i.json.gz
appender.index_search_slowlog_rolling.policies.type = Policies
appender.index_search_slowlog_rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.index_search_slowlog_rolling.policies.size.size = 1GB
appender.index_search_slowlog_rolling.strategy.type = DefaultRolloverStrategy
appender.index_search_slowlog_rolling.strategy.max = 4
#################################################
######## Search slowlog - old style pattern ####
appender.index_search_slowlog_rolling_old.type = RollingFile
appender.index_search_slowlog_rolling_old.name = index_search_slowlog_rolling_old
appender.index_search_slowlog_rolling_old.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}\
_index_search_slowlog.log
appender.index_search_slowlog_rolling_old.layout.type = PatternLayout
appender.index_search_slowlog_rolling_old.layout.pattern = [%d{ISO8601}][%-5p][%-25c{1.}] [%node_name]%marker %m%n
appender.index_search_slowlog_rolling_old.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}\
_index_search_slowlog-%i.log.gz
appender.index_search_slowlog_rolling_old.policies.type = Policies
appender.index_search_slowlog_rolling_old.policies.size.type = SizeBasedTriggeringPolicy
appender.index_search_slowlog_rolling_old.policies.size.size = 1GB
appender.index_search_slowlog_rolling_old.strategy.type = DefaultRolloverStrategy
appender.index_search_slowlog_rolling_old.strategy.max = 4
#################################################
logger.index_search_slowlog_rolling.name = index.search.slowlog
logger.index_search_slowlog_rolling.level = trace
logger.index_search_slowlog_rolling.appenderRef.index_search_slowlog_rolling.ref = index_search_slowlog_rolling
logger.index_search_slowlog_rolling.appenderRef.index_search_slowlog_rolling_old.ref = index_search_slowlog_rolling_old
logger.index_search_slowlog_rolling.additivity = false
######## Indexing slowlog JSON ##################
appender.index_indexing_slowlog_rolling.type = RollingFile
appender.index_indexing_slowlog_rolling.name = index_indexing_slowlog_rolling
appender.index_indexing_slowlog_rolling.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}\
_index_indexing_slowlog.json
appender.index_indexing_slowlog_rolling.layout.type = ESJsonLayout
appender.index_indexing_slowlog_rolling.layout.type_name = index_indexing_slowlog
appender.index_indexing_slowlog_rolling.layout.esmessagefields=message,took,took_millis,doc_type,id,routing,source
appender.index_indexing_slowlog_rolling.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}\
_index_indexing_slowlog-%i.json.gz
appender.index_indexing_slowlog_rolling.policies.type = Policies
appender.index_indexing_slowlog_rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.index_indexing_slowlog_rolling.policies.size.size = 1GB
appender.index_indexing_slowlog_rolling.strategy.type = DefaultRolloverStrategy
appender.index_indexing_slowlog_rolling.strategy.max = 4
#################################################
######## Indexing slowlog - old style pattern ##
appender.index_indexing_slowlog_rolling_old.type = RollingFile
appender.index_indexing_slowlog_rolling_old.name = index_indexing_slowlog_rolling_old
appender.index_indexing_slowlog_rolling_old.fileName = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}\
_index_indexing_slowlog.log
appender.index_indexing_slowlog_rolling_old.layout.type = PatternLayout
appender.index_indexing_slowlog_rolling_old.layout.pattern = [%d{ISO8601}][%-5p][%-25c{1.}] [%node_name]%marker %m%n
appender.index_indexing_slowlog_rolling_old.filePattern = ${sys:es.logs.base_path}${sys:file.separator}${sys:es.logs.cluster_name}\
_index_indexing_slowlog-%i.log.gz
appender.index_indexing_slowlog_rolling_old.policies.type = Policies
appender.index_indexing_slowlog_rolling_old.policies.size.type = SizeBasedTriggeringPolicy
appender.index_indexing_slowlog_rolling_old.policies.size.size = 1GB
appender.index_indexing_slowlog_rolling_old.strategy.type = DefaultRolloverStrategy
appender.index_indexing_slowlog_rolling_old.strategy.max = 4
#################################################
logger.index_indexing_slowlog.name = index.indexing.slowlog.index
logger.index_indexing_slowlog.level = trace
logger.index_indexing_slowlog.appenderRef.index_indexing_slowlog_rolling.ref = index_indexing_slowlog_rolling
logger.index_indexing_slowlog.appenderRef.index_indexing_slowlog_rolling_old.ref = index_indexing_slowlog_rolling_old
logger.index_indexing_slowlog.additivity = false

16
ELK.Docker/shared/config-elk/filebeat/config/filebeat.yml Normal file
View File

@ -0,0 +1,16 @@
#filebeat.registry_file: /usr/share/filebeat/registry
filebeat.inputs:
- type: log
paths:
- /usr/share/filebeat/log_data/dmp/openDMP*.log
tags: ["audit"]
enabled: true
reload.enabled: true
reload.period: 10s
multiline.pattern: '^[0-9]{4}-[0-9]{2}-[0-9]{2}'
multiline.negate: true
multiline.match: after
output.logstash:
hosts: ["logstash:31312"]
bulk_max_size: 128

17
ELK.Docker/shared/config-elk/kibana/config/kibana.yml Normal file
View File

@ -0,0 +1,17 @@
---
## Default Kibana configuration from kibana-docker.
## from https://github.com/elastic/kibana-docker/blob/master/build/kibana/config/kibana.yml
#
server.name: kibana
server.host: "0"
## Custom configuration
#
#server.basePath: "/eformslogs"
elasticsearch.hosts: [ "http://elasticsearch:9200" ]
#elasticsearch.ssl.certificateAuthorities: [ "/usr/share/kibana/certificate_authorities/ca.crt" ]
elasticsearch.username: "kibana"
elasticsearch.password: ""
server.ssl.enabled: false
#server.ssl.key: "/usr/share/kibana/certificates/kibana.key"
#server.ssl.certificate: "/usr/share/kibana/certificates/kibana.crt"

103
ELK.Docker/shared/config-elk/logstash/config/log4j2.properties Normal file
View File

@ -0,0 +1,103 @@
#https://github.com/elastic/logstash/blob/7.4/config/log4j2.properties
status = error
name = LogstashPropertiesConfig
appender.console.type = Console
appender.console.name = plain_console
appender.console.layout.type = PatternLayout
appender.console.layout.pattern = [%d{ISO8601}][%-5p][%-25c]%notEmpty{[%X{pipeline.id}]} %m%n
appender.json_console.type = Console
appender.json_console.name = json_console
appender.json_console.layout.type = JSONLayout
appender.json_console.layout.compact = true
appender.json_console.layout.eventEol = true
appender.rolling.type = RollingFile
appender.rolling.name = plain_rolling
appender.rolling.fileName = ${sys:ls.logs}/logstash-${sys:ls.log.format}.log
appender.rolling.filePattern = ${sys:ls.logs}/logstash-${sys:ls.log.format}-%d{yyyy-MM-dd}-%i.log.gz
appender.rolling.policies.type = Policies
appender.rolling.policies.time.type = TimeBasedTriggeringPolicy
appender.rolling.policies.time.interval = 1
appender.rolling.policies.time.modulate = true
appender.rolling.layout.type = PatternLayout
appender.rolling.layout.pattern = [%d{ISO8601}][%-5p][%-25c]%notEmpty{[%X{pipeline.id}]} %m%n
appender.rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.rolling.policies.size.size = 100MB
appender.rolling.strategy.type = DefaultRolloverStrategy
appender.rolling.strategy.max = 30
appender.json_rolling.type = RollingFile
appender.json_rolling.name = json_rolling
appender.json_rolling.fileName = ${sys:ls.logs}/logstash-${sys:ls.log.format}.log
appender.json_rolling.filePattern = ${sys:ls.logs}/logstash-${sys:ls.log.format}-%d{yyyy-MM-dd}-%i.log.gz
appender.json_rolling.policies.type = Policies
appender.json_rolling.policies.time.type = TimeBasedTriggeringPolicy
appender.json_rolling.policies.time.interval = 1
appender.json_rolling.policies.time.modulate = true
appender.json_rolling.layout.type = JSONLayout
appender.json_rolling.layout.compact = true
appender.json_rolling.layout.eventEol = true
appender.json_rolling.policies.size.type = SizeBasedTriggeringPolicy
appender.json_rolling.policies.size.size = 100MB
appender.json_rolling.strategy.type = DefaultRolloverStrategy
appender.json_rolling.strategy.max = 30
rootLogger.level = ${sys:ls.log.level}
rootLogger.appenderRef.console.ref = ${sys:ls.log.format}_console
rootLogger.appenderRef.rolling.ref = ${sys:ls.log.format}_rolling
# Slowlog
appender.console_slowlog.type = Console
appender.console_slowlog.name = plain_console_slowlog
appender.console_slowlog.layout.type = PatternLayout
appender.console_slowlog.layout.pattern = [%d{ISO8601}][%-5p][%-25c] %m%n
appender.json_console_slowlog.type = Console
appender.json_console_slowlog.name = json_console_slowlog
appender.json_console_slowlog.layout.type = JSONLayout
appender.json_console_slowlog.layout.compact = true
appender.json_console_slowlog.layout.eventEol = true
appender.rolling_slowlog.type = RollingFile
appender.rolling_slowlog.name = plain_rolling_slowlog
appender.rolling_slowlog.fileName = ${sys:ls.logs}/logstash-slowlog-${sys:ls.log.format}.log
appender.rolling_slowlog.filePattern = ${sys:ls.logs}/logstash-slowlog-${sys:ls.log.format}-%d{yyyy-MM-dd}-%i.log.gz
appender.rolling_slowlog.policies.type = Policies
appender.rolling_slowlog.policies.time.type = TimeBasedTriggeringPolicy
appender.rolling_slowlog.policies.time.interval = 1
appender.rolling_slowlog.policies.time.modulate = true
appender.rolling_slowlog.layout.type = PatternLayout
appender.rolling_slowlog.layout.pattern = [%d{ISO8601}][%-5p][%-25c] %m%n
appender.rolling_slowlog.policies.size.type = SizeBasedTriggeringPolicy
appender.rolling_slowlog.policies.size.size = 100MB
appender.rolling_slowlog.strategy.type = DefaultRolloverStrategy
appender.rolling_slowlog.strategy.max = 30
appender.json_rolling_slowlog.type = RollingFile
appender.json_rolling_slowlog.name = json_rolling_slowlog
appender.json_rolling_slowlog.fileName = ${sys:ls.logs}/logstash-slowlog-${sys:ls.log.format}.log
appender.json_rolling_slowlog.filePattern = ${sys:ls.logs}/logstash-slowlog-${sys:ls.log.format}-%d{yyyy-MM-dd}-%i.log.gz
appender.json_rolling_slowlog.policies.type = Policies
appender.json_rolling_slowlog.policies.time.type = TimeBasedTriggeringPolicy
appender.json_rolling_slowlog.policies.time.interval = 1
appender.json_rolling_slowlog.policies.time.modulate = true
appender.json_rolling_slowlog.layout.type = JSONLayout
appender.json_rolling_slowlog.layout.compact = true
appender.json_rolling_slowlog.layout.eventEol = true
appender.json_rolling_slowlog.policies.size.type = SizeBasedTriggeringPolicy
appender.json_rolling_slowlog.policies.size.size = 100MB
appender.json_rolling_slowlog.strategy.type = DefaultRolloverStrategy
appender.json_rolling_slowlog.strategy.max = 30
logger.slowlog.name = slowlog
logger.slowlog.level = trace
logger.slowlog.appenderRef.console_slowlog.ref = ${sys:ls.log.format}_console_slowlog
logger.slowlog.appenderRef.rolling_slowlog.ref = ${sys:ls.log.format}_rolling_slowlog
logger.slowlog.additivity = false
logger.licensereader.name = logstash.licensechecker.licensereader
logger.licensereader.level = error

10
ELK.Docker/shared/config-elk/logstash/config/logstash.yml Normal file
View File

@ -0,0 +1,10 @@
---
## Default Logstash configuration from logstash-docker.
## from https://github.com/elastic/logstash-docker/blob/master/build/logstash/config/logstash-oss.yml
#
http.host: "0.0.0.0"
config.reload.automatic: true
config.reload.interval: 300s
path.queue: /usr/share/logstash/queue
path.dead_letter_queue: /usr/share/logstash/dead_letter_queue
xpack.monitoring.elasticsearch.password:

18
ELK.Docker/shared/config-elk/logstash/config/pipelines.yml Normal file
View File

@ -0,0 +1,18 @@
- pipeline.id: open_dmp_beats
queue.type: persisted
queue.max_bytes: 50mb
dead_letter_queue.enable: true
path.config: "/usr/share/logstash/pipeline/open_dmp_beats.conf"
queue.checkpoint.writes: 32
- pipeline.id: open_dmp_main
queue.type: persisted
queue.max_bytes: 50mb
dead_letter_queue.enable: true
path.config: "/usr/share/logstash/pipeline/open_dmp_main.conf"
queue.checkpoint.writes: 32
- pipeline.id: open_dmp_send_to_elastic
queue.type: persisted
queue.max_bytes: 50mb
dead_letter_queue.enable: true
path.config: "/usr/share/logstash/pipeline/open_dmp_send_to_elastic.conf"
queue.checkpoint.writes: 32

14
ELK.Docker/shared/config-elk/logstash/pipeline/open_dmp_beats.conf Normal file
View File

@ -0,0 +1,14 @@
input {
beats {
port => 31312
ssl => false
client_inactivity_timeout => 3000
}
}
filter {
}
output {
pipeline { send_to => open_dmp_main }
}

19
ELK.Docker/shared/config-elk/logstash/pipeline/open_dmp_main.conf Normal file
View File

@ -0,0 +1,19 @@
input {
pipeline { address => open_dmp_main }
}
filter {
grok {
match => { "message" => "(?<timestamp>%{DATE} %{TIME})%{SPACE}%{LOGLEVEL:level} %{NUMBER:pid} --- \[%{DATA:thread}\] %{DATA:class}%{SPACE}: %{GREEDYDATA:logmessage}" }
}
if "_grokparsefailure" not in [tags] {
mutate
{
remove_field => [ "message" ]
}
}
}
output {
pipeline { send_to => open_dmp_send_to_elastic }
}

19
ELK.Docker/shared/config-elk/logstash/pipeline/open_dmp_send_to_elastic.conf Normal file
View File

@ -0,0 +1,19 @@
input {
pipeline { address => open_dmp_send_to_elastic }
}
filter {
}
output {
elasticsearch {
hosts => "elasticsearch:9200"
user => elastic
password =>
index =>"opendmp.logs"
#manage_template => true
#template => "/usr/share/logstash/templates/audit/cite_elas_openDMP.json"
#template_name => "cite.elas.openDMP-audit*"
#template_overwrite => true
}
}

0
ELK.Docker/shared/data-elk/elasticsearch-01-data/.gitkeep Normal file
View File

0
ELK.Docker/shared/data-elk/elasticsearch-01-log/.gitkeep Normal file
View File

0
ELK.Docker/shared/data-elk/filebeat-data/.gitkeep Normal file
View File

0
ELK.Docker/shared/data-elk/filebeat-log/.gitkeep Normal file
View File

0
ELK.Docker/shared/data-elk/logstash-dead_letter_queue/.gitkeep Normal file
View File

0
ELK.Docker/shared/data-elk/logstash-log/.gitkeep Normal file
View File

0
ELK.Docker/shared/data-elk/logstash-queue/.gitkeep Normal file
View File

1
dmp-backend/data/pom.xml
View File

@ -4,7 +4,6 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.eudat</groupId>
<artifactId>data</artifactId>
<version>1.0-SNAPSHOT</version>
<packaging>jar</packaging>

19
dmp-backend/data/src/main/java/eu/eudat/data/dao/criteria/DatasetCriteria.java
View File

@ -2,6 +2,7 @@ package eu.eudat.data.dao.criteria;
import eu.eudat.data.entities.Dataset;
import eu.eudat.elastic.entities.Tag;
import eu.eudat.types.grant.GrantStateType;
import java.util.Date;
import java.util.List;
@ -22,6 +23,8 @@ public class DatasetCriteria extends Criteria<Dataset> {
private List<UUID> collaborators;
private List<UUID> datasetTemplates;
private List<UUID> groupIds;
private Boolean isPublic;
private Short grantStatus;
public boolean getAllVersions() {
return allVersions;
@ -113,4 +116,20 @@ public class DatasetCriteria extends Criteria<Dataset> {
public void setGroupIds(List<UUID> groupIds) {
this.groupIds = groupIds;
}
public Boolean getIsPublic() {
return isPublic;
}
public void setIsPublic(Boolean isPublic) {
this.isPublic = isPublic;
}
public Short getGrantStatus() {
return grantStatus;
}
public void setGrantStatus(Short grantStatus) {
this.grantStatus = grantStatus;
}
}

38
dmp-backend/data/src/main/java/eu/eudat/data/dao/criteria/LockCriteria.java Normal file
View File

@ -0,0 +1,38 @@
package eu.eudat.data.dao.criteria;
import eu.eudat.data.entities.Lock;
import eu.eudat.data.entities.UserInfo;
import java.util.Date;
import java.util.UUID;
public class LockCriteria extends Criteria<Lock> {
private UUID target;
private UserInfo lockedBy;
private Date touchedAt;
public UUID getTarget() {
return target;
}
public void setTarget(UUID target) {
this.target = target;
}
public UserInfo getLockedBy() {
return lockedBy;
}
public void setLockedBy(UserInfo lockedBy) {
this.lockedBy = lockedBy;
}
public Date getTouchedAt() {
return touchedAt;
}
public void setTouchedAt(Date touchedAt) {
this.touchedAt = touchedAt;
}
}

26
dmp-backend/data/src/main/java/eu/eudat/data/dao/criteria/NotificationCriteria.java Normal file
View File

@ -0,0 +1,26 @@
package eu.eudat.data.dao.criteria;
import eu.eudat.data.enumeration.notification.ActiveStatus;
import eu.eudat.data.enumeration.notification.NotifyState;
public class NotificationCriteria {
private ActiveStatus isActive;
private NotifyState notifyState;
public ActiveStatus getIsActive() {
return isActive;
}
public void setIsActive(ActiveStatus isActive) {
this.isActive = isActive;
}
public NotifyState getNotifyState() {
return notifyState;
}
public void setNotifyState(NotifyState notifyState) {
this.notifyState = notifyState;
}
}

5
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/DMPDaoImpl.java
View File

@ -43,8 +43,9 @@ public class DMPDaoImpl extends DatabaseAccess<DMP> implements DMPDao {
query.where(((builder, root) -> root.get("grant").in(criteria.getGrants())));
if (!criteria.getAllVersions())
query.initSubQuery(String.class).where((builder, root) -> builder.equal(root.get("version"),
query.<String>subQueryMax((builder1, externalRoot, nestedRoot) -> builder1.equal(externalRoot.get("groupId"),
nestedRoot.get("groupId")), Arrays.asList(new SelectionField(FieldSelectionType.FIELD, "version")), String.class)));
query.<String>subQueryMax((builder1, externalRoot, nestedRoot) -> builder1.and(
builder1.equal(externalRoot.get("groupId"), nestedRoot.get("groupId")),
builder1.notEqual(nestedRoot.get("status"), DMP.DMPStatus.DELETED.getValue())), Arrays.asList(new SelectionField(FieldSelectionType.FIELD, "version")), String.class)));
if (criteria.getGroupIds() != null && !criteria.getGroupIds().isEmpty())
query.where((builder, root) -> root.get("groupId").in(criteria.getGroupIds()));
if (criteria.getStatus() != null) {

20
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/DatasetDaoImpl.java
View File

@ -3,12 +3,14 @@ package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.criteria.DatasetCriteria;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.UserDMP;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.queryable.QueryableList;
import eu.eudat.queryable.types.FieldSelectionType;
import eu.eudat.queryable.types.SelectionField;
import eu.eudat.types.grant.GrantStateType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.annotation.Async;
import org.springframework.stereotype.Component;
@ -16,6 +18,7 @@ import org.springframework.stereotype.Component;
import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@ -29,6 +32,13 @@ public class DatasetDaoImpl extends DatabaseAccess<Dataset> implements DatasetDa
@Override
public QueryableList<Dataset> getWithCriteria(DatasetCriteria criteria) {
QueryableList<Dataset> query = getDatabaseService().getQueryable(Dataset.getHints(), Dataset.class);
if (criteria.getIsPublic() != null && criteria.getIsPublic()) {
query.where((builder, root) -> builder.equal(root.get("dmp").get("isPublic"), true));
query.where((builder, root) -> builder.equal(root.get("status"), Dataset.Status.FINALISED.getValue()));
query.initSubQuery(String.class).where((builder, root) -> builder.equal(root.get("dmp").get("version"),
query.<String>subQueryMax((builder1, externalRoot, nestedRoot) -> builder1.equal(externalRoot.get("dmp").get("groupId"), nestedRoot.get("dmp").get("groupId")),
Arrays.asList(new SelectionField(FieldSelectionType.COMPOSITE_FIELD, "dmp:version")), String.class)));
}
if (criteria.getLike() != null && !criteria.getLike().isEmpty())
query.where((builder, root) -> builder.or(
builder.like(builder.upper(root.get("label")), "%" + criteria.getLike().toUpperCase() + "%"),
@ -42,7 +52,7 @@ public class DatasetDaoImpl extends DatabaseAccess<Dataset> implements DatasetDa
if (criteria.getPeriodStart() != null)
query.where((builder, root) -> builder.greaterThan(root.get("created"), criteria.getPeriodStart()));
if (!criteria.getAllVersions())
query.initSubQuery(String.class).where((builder, root) -> builder.equal(root.get("dmp").get("version"), query.<String>subQueryMax((builder1, externalRoot, nestedRoot) -> builder1.equal(externalRoot.get("dmp").get("groupId"), nestedRoot.get("dmp").get("groupId")), Arrays.asList(new SelectionField(FieldSelectionType.COMPOSITE_FIELD, "dmp:version")), String.class)));
query.initSubQuery(String.class).where((builder, root) -> builder.equal(root.get("dmp").get("version"), query.<String>subQueryMax((builder1, externalRoot, nestedRoot) -> builder1.and(builder1.equal(externalRoot.get("dmp").get("groupId"), nestedRoot.get("dmp").get("groupId")), builder1.notEqual(nestedRoot.get("dmp").get("status"), DMP.DMPStatus.DELETED.getValue())), Arrays.asList(new SelectionField(FieldSelectionType.COMPOSITE_FIELD, "dmp:version")), String.class)));
if (criteria.getGroupIds() != null && !criteria.getGroupIds().isEmpty())
query.where((builder, root) -> root.get("dmp").get("groupId").in(criteria.getGroupIds()));
if (criteria.getDmpIds() != null && !criteria.getDmpIds().isEmpty())
@ -56,6 +66,14 @@ public class DatasetDaoImpl extends DatabaseAccess<Dataset> implements DatasetDa
query.where((builder, root) -> root.join("dmp").join("organisations").get("reference").in(criteria.getOrganisations()));
if (criteria.getGrants() != null && !criteria.getGrants().isEmpty())
query.where((builder, root) -> root.join("dmp").join("grant").get("id").in(criteria.getGrants()));
if (criteria.getGrantStatus() != null) {
if (criteria.getGrantStatus().equals(GrantStateType.FINISHED.getValue().shortValue()))
query.where((builder, root) -> builder.lessThan(root.get("dmp").get("grant").get("enddate"), new Date()));
if (criteria.getGrantStatus().equals(GrantStateType.ONGOING.getValue().shortValue()))
query.where((builder, root) ->
builder.or(builder.greaterThan(root.get("dmp").get("grant").get("enddate"), new Date())
, builder.isNull(root.get("dmp").get("grant").get("enddate"))));
}
if (criteria.getCollaborators() != null && !criteria.getCollaborators().isEmpty())
query.where((builder, root) -> root.join("dmp", JoinType.LEFT).join("users", JoinType.LEFT).join("user", JoinType.LEFT).get("id").in(criteria.getCollaborators()));
if (criteria.getDatasetTemplates() != null && !criteria.getDatasetTemplates().isEmpty())

13
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/LockDao.java Normal file
View File

@ -0,0 +1,13 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.dao.criteria.LockCriteria;
import eu.eudat.data.entities.Lock;
import eu.eudat.queryable.QueryableList;
import java.util.UUID;
public interface LockDao extends DatabaseAccessLayer<Lock, UUID> {
QueryableList<Lock> getWithCriteria(LockCriteria criteria);
}

65
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/LockDaoImpl.java Normal file
View File

@ -0,0 +1,65 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.criteria.LockCriteria;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.Lock;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.annotation.Async;
import org.springframework.stereotype.Service;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@Service("LockDao")
public class LockDaoImpl extends DatabaseAccess<Lock> implements LockDao {
@Autowired
public LockDaoImpl(DatabaseService<Lock> databaseService) {
super(databaseService);
}
@Override
public QueryableList<Lock> getWithCriteria(LockCriteria criteria) {
QueryableList<Lock> query = this.getDatabaseService().getQueryable(Lock.class);
if (criteria.getTouchedAt() != null)
query.where((builder, root) -> builder.equal(root.get("touchedAt"), criteria.getTouchedAt()));
if (criteria.getLockedBy() != null)
query.where(((builder, root) -> builder.equal(root.get("lockedBy"), criteria.getLockedBy())));
if (criteria.getTarget() != null)
query.where(((builder, root) -> builder.equal(root.get("target"), criteria.getTarget())));
return query;
}
@Override
public Lock createOrUpdate(Lock item) {
return this.getDatabaseService().createOrUpdate(item, Lock.class);
}
@Async
@Override
public CompletableFuture<Lock> createOrUpdateAsync(Lock item) {
return CompletableFuture.supplyAsync(() -> this.createOrUpdate(item));
}
@Override
public Lock find(UUID id) {
return this.getDatabaseService().getQueryable(Lock.class).where(((builder, root) -> builder.equal(root.get("id"), id))).getSingle();
}
@Override
public Lock find(UUID id, String hint) {
throw new UnsupportedOperationException();
}
@Override
public void delete(Lock item) {
this.getDatabaseService().delete(item);
}
@Override
public QueryableList<Lock> asQueryable() {
return this.getDatabaseService().getQueryable(Lock.class);
}
}

13
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/NotificationDao.java Normal file
View File

@ -0,0 +1,13 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.dao.criteria.NotificationCriteria;
import eu.eudat.data.entities.Notification;
import eu.eudat.queryable.QueryableList;
import java.util.UUID;
public interface NotificationDao extends DatabaseAccessLayer<Notification, UUID> {
QueryableList<Notification> getWithCriteria(NotificationCriteria criteria);
}

61
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/NotificationDaoImpl.java Normal file
View File

@ -0,0 +1,61 @@
package eu.eudat.data.dao.entities;
import eu.eudat.data.dao.DatabaseAccess;
import eu.eudat.data.dao.criteria.NotificationCriteria;
import eu.eudat.data.dao.databaselayer.service.DatabaseService;
import eu.eudat.data.entities.Lock;
import eu.eudat.data.entities.Notification;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@Service("NotificationDao")
public class NotificationDaoImpl extends DatabaseAccess<Notification> implements NotificationDao {
@Autowired
public NotificationDaoImpl(DatabaseService<Notification> databaseService) {
super(databaseService);
}
@Override
public QueryableList<Notification> getWithCriteria(NotificationCriteria criteria) {
QueryableList<Notification> query = this.getDatabaseService().getQueryable(Notification.class);
if (criteria.getIsActive() != null)
query.where((builder, root) -> builder.equal(root.get("isActive"), criteria.getIsActive()));
if (criteria.getNotifyState() != null)
query.where(((builder, root) -> builder.equal(root.get("notifyState"), criteria.getNotifyState())));
return query;
}
@Override
public Notification createOrUpdate(Notification item) {
return this.getDatabaseService().createOrUpdate(item, Notification.class);
}
@Override
public CompletableFuture<Notification> createOrUpdateAsync(Notification item) {
return CompletableFuture.supplyAsync(() -> this.getDatabaseService().createOrUpdate(item, Notification.class));
}
@Override
public Notification find(UUID id) {
return this.getDatabaseService().getQueryable(Notification.class).where(((builder, root) -> builder.equal(root.get("id"), id))).getSingle();
}
@Override
public Notification find(UUID id, String hint) {
throw new UnsupportedOperationException();
}
@Override
public void delete(Notification item) {
this.getDatabaseService().delete(item);
}
@Override
public QueryableList<Notification> asQueryable() {
return this.getDatabaseService().getQueryable(Notification.class);
}
}

95
dmp-backend/data/src/main/java/eu/eudat/data/entities/Lock.java Normal file
View File

@ -0,0 +1,95 @@
package eu.eudat.data.entities;
import eu.eudat.data.converters.DateToUTCConverter;
import eu.eudat.data.entities.helpers.EntityBinder;
import eu.eudat.queryable.queryableentity.DataEntity;
import org.hibernate.annotations.GenericGenerator;
import javax.persistence.*;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@Entity
@Table(name = "\"Lock\"")
public class Lock implements DataEntity<Lock, UUID> {
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
@Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;
@Column(name = "\"Target\"", nullable = false)
private UUID target;
@ManyToOne(fetch = FetchType.EAGER)
@JoinColumn(name = "\"LockedBy\"", nullable = false)
private UserInfo lockedBy;
@Column(name = "\"LockedAt\"")
@Convert(converter = DateToUTCConverter.class)
private Date lockedAt = new Date();
@Column(name = "\"TouchedAt\"")
@Convert(converter = DateToUTCConverter.class)
private Date touchedAt = null;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public UUID getTarget() {
return target;
}
public void setTarget(UUID target) {
this.target = target;
}
public UserInfo getLockedBy() {
return lockedBy;
}
public void setLockedBy(UserInfo lockedBy) {
this.lockedBy = lockedBy;
}
public Date getLockedAt() {
return lockedAt;
}
public void setLockedAt(Date lockedAt) {
this.lockedAt = lockedAt;
}
public Date getTouchedAt() {
return touchedAt;
}
public void setTouchedAt(Date touchedAt) {
this.touchedAt = touchedAt;
}
@Override
public void update(Lock entity) {
this.touchedAt = entity.touchedAt;
}
@Override
public UUID getKeys() {
return this.id;
}
@Override
public Lock buildFromTuple(List<Tuple> tuple, List<String> fields, String base) {
String currentBase = base.isEmpty() ? "" : base + ".";
if (fields.contains(currentBase + "id")) this.id = EntityBinder.fromTuple(tuple, currentBase + "id");
return this;
}
}

175
dmp-backend/data/src/main/java/eu/eudat/data/entities/Notification.java Normal file
View File

@ -0,0 +1,175 @@
package eu.eudat.data.entities;
import eu.eudat.data.enumeration.notification.ActiveStatus;
import eu.eudat.data.enumeration.notification.ContactType;
import eu.eudat.data.enumeration.notification.NotificationType;
import eu.eudat.data.enumeration.notification.NotifyState;
import eu.eudat.queryable.queryableentity.DataEntity;
import org.hibernate.annotations.GenericGenerator;
import javax.persistence.*;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@Entity
@Table(name = "\"Notification\"")
public class Notification implements DataEntity<Notification, UUID> {
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
@Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;
@ManyToOne(fetch = FetchType.EAGER)
@JoinColumn(name = "\"UserId\"")
private UserInfo userId;
@Enumerated
@Column(name = "\"IsActive\"", nullable = false)
private ActiveStatus isActive;
@Enumerated
@Column(name = "\"Type\"", nullable = false)
private NotificationType type;
@Enumerated
@Column(name = "\"ContactTypeHint\"")
private ContactType contactTypeHint;
@Column(name = "\"ContactHint\"")
private String contactHint;
@Column(name = "\"Data\"")
private String data;
@Enumerated
@Column(name = "\"NotifyState\"")
private NotifyState notifyState;
@Column(name = "\"NotifiedAt\"")
private Date notifiedAt;
@Column(name = "\"RetryCount\"")
private Integer retryCount;
@Column(name = "\"CreatedAt\"")
private Date createdAt;
@Column(name = "\"UpdatedAt\"")
private Date updatedAt;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public UserInfo getUserId() {
return userId;
}
public void setUserId(UserInfo userId) {
this.userId = userId;
}
public ActiveStatus getIsActive() {
return isActive;
}
public void setIsActive(ActiveStatus isActive) {
this.isActive = isActive;
}
public NotificationType getType() {
return type;
}
public void setType(NotificationType type) {
this.type = type;
}
public ContactType getContactTypeHint() {
return contactTypeHint;
}
public void setContactTypeHint(ContactType contactTypeHint) {
this.contactTypeHint = contactTypeHint;
}
public String getContactHint() {
return contactHint;
}
public void setContactHint(String contactHint) {
this.contactHint = contactHint;
}
public String getData() {
return data;
}
public void setData(String data) {
this.data = data;
}
public NotifyState getNotifyState() {
return notifyState;
}
public void setNotifyState(NotifyState notifyState) {
this.notifyState = notifyState;
}
public Date getNotifiedAt() {
return notifiedAt;
}
public void setNotifiedAt(Date notifiedAt) {
this.notifiedAt = notifiedAt;
}
public Integer getRetryCount() {
return retryCount;
}
public void setRetryCount(Integer retryCount) {
this.retryCount = retryCount;
}
public Date getCreatedAt() {
return createdAt;
}
public void setCreatedAt(Date createdAt) {
this.createdAt = createdAt;
}
public Date getUpdatedAt() {
return updatedAt;
}
public void setUpdatedAt(Date updatedAt) {
this.updatedAt = updatedAt;
}
@Override
public void update(Notification entity) {
}
@Override
public UUID getKeys() {
return null;
}
@Override
public Notification buildFromTuple(List<Tuple> tuple, List<String> fields, String base) {
return null;
}
}

22
dmp-backend/data/src/main/java/eu/eudat/data/entities/UserInfo.java
View File

@ -69,6 +69,12 @@ public class UserInfo implements DataEntity<UserInfo, UUID> {
@OneToMany(mappedBy = "userInfo", fetch = FetchType.LAZY)
private Set<UserRole> userRoles = new HashSet<>();
@OneToMany(mappedBy = "lockedBy", fetch = FetchType.LAZY)
private Set<Lock> locks = new HashSet<>();
@OneToMany(mappedBy = "userId", fetch = FetchType.LAZY)
private Set<Notification> notifications = new HashSet<>();
public Set<DMP> getDmps() {
return dmps;
}
@ -165,6 +171,22 @@ public class UserInfo implements DataEntity<UserInfo, UUID> {
this.userRoles = userRoles;
}
public Set<Lock> getLocks() {
return locks;
}
public void setLocks(Set<Lock> locks) {
this.locks = locks;
}
public Set<Notification> getNotifications() {
return notifications;
}
public void setNotifications(Set<Notification> notifications) {
this.notifications = notifications;
}
@Override
public void update(UserInfo entity) {
this.name = entity.getName();

27
dmp-backend/data/src/main/java/eu/eudat/data/enumeration/notification/ActiveStatus.java Normal file
View File

@ -0,0 +1,27 @@
package eu.eudat.data.enumeration.notification;
public enum ActiveStatus {
ACTIVE(0),
INACTIVE(1);
private int status;
ActiveStatus(int status) {
this.status = status;
}
public int getStatus() {
return status;
}
public ActiveStatus fromInteger(int status) {
switch (status) {
case 0:
return ACTIVE;
case 1:
return INACTIVE;
default:
throw new RuntimeException("Unsupported Active Status");
}
}
}

24
dmp-backend/data/src/main/java/eu/eudat/data/enumeration/notification/ContactType.java Normal file
View File

@ -0,0 +1,24 @@
package eu.eudat.data.enumeration.notification;
public enum ContactType {
EMAIL(0);
private int type;
ContactType(int type) {
this.type = type;
}
public int getType() {
return type;
}
public ContactType fromInteger(int type) {
switch (type) {
case 0:
return EMAIL;
default:
throw new RuntimeException("Unsupported Contact Type");
}
}
}

39
dmp-backend/data/src/main/java/eu/eudat/data/enumeration/notification/NotificationType.java Normal file
View File

@ -0,0 +1,39 @@
package eu.eudat.data.enumeration.notification;
public enum NotificationType {
DMP_MODIFIED(0),
DATASET_MODIFIED(1),
DMP_PUBLISH(2),
DMP_FINALISED(3),
DMP_MODIFIED_FINALISED(4),
DATASET_MODIFIED_FINALISED(5);
private int type;
NotificationType(int type) {
this.type = type;
}
public int getType() {
return type;
}
public NotificationType fromInteger(int type) {
switch (type) {
case 0:
return DMP_MODIFIED;
case 1:
return DATASET_MODIFIED;
case 2:
return DMP_PUBLISH;
case 3:
return DMP_FINALISED;
case 4:
return DMP_MODIFIED_FINALISED;
case 5:
return DATASET_MODIFIED_FINALISED;
default:
throw new RuntimeException("Unsupported Notification Type");
}
}
}

36
dmp-backend/data/src/main/java/eu/eudat/data/enumeration/notification/NotifyState.java Normal file
View File

@ -0,0 +1,36 @@
package eu.eudat.data.enumeration.notification;
public enum NotifyState {
PENDING(0),
PROCESSING(1),
SENDING(2),
SUCCEEDED(3),
ERROR(4);
private int state;
NotifyState(int state) {
this.state = state;
}
public int getState() {
return state;
}
public NotifyState fromInteger(int state) {
switch (state) {
case 0:
return PENDING;
case 1:
return PROCESSING;
case 2:
return SENDING;
case 3:
return SUCCEEDED;
case 4:
return ERROR;
default:
throw new RuntimeException("Unsupported Notify State");
}
}
}

20
dmp-backend/data/src/main/java/eu/eudat/data/query/items/item/lock/LockCriteriaRequest.java Normal file
View File

@ -0,0 +1,20 @@
package eu.eudat.data.query.items.item.lock;
import eu.eudat.data.dao.criteria.LockCriteria;
import eu.eudat.data.entities.Lock;
import eu.eudat.data.query.definition.Query;
import eu.eudat.queryable.QueryableList;
public class LockCriteriaRequest extends Query<LockCriteria, Lock> {
@Override
public QueryableList<Lock> applyCriteria() {
QueryableList<Lock> query = this.getQuery();
if (this.getCriteria().getTouchedAt() != null)
query.where((builder, root) -> builder.equal(root.get("touchedAt"), this.getCriteria().getTouchedAt()));
if (this.getCriteria().getLockedBy() != null)
query.where(((builder, root) -> builder.equal(root.get("lockedBy"), this.getCriteria().getLockedBy())));
if (this.getCriteria().getTarget() != null)
query.where(((builder, root) -> builder.equal(root.get("target"), this.getCriteria().getTarget())));
return query;
}
}

29
dmp-backend/data/src/main/java/eu/eudat/data/query/items/table/lock/LockTableRequest.java Normal file
View File

@ -0,0 +1,29 @@
package eu.eudat.data.query.items.table.lock;
import eu.eudat.data.dao.criteria.LockCriteria;
import eu.eudat.data.entities.Lock;
import eu.eudat.data.query.PaginationService;
import eu.eudat.data.query.definition.Query;
import eu.eudat.data.query.definition.TableQuery;
import eu.eudat.queryable.QueryableList;
import java.util.UUID;
public class LockTableRequest extends TableQuery<LockCriteria, Lock, UUID> {
@Override
public QueryableList<Lock> applyCriteria() {
QueryableList<Lock> query = this.getQuery();
if (this.getCriteria().getTouchedAt() != null)
query.where((builder, root) -> builder.equal(root.get("touchedAt"), this.getCriteria().getTouchedAt()));
if (this.getCriteria().getLockedBy() != null)
query.where(((builder, root) -> builder.equal(root.get("lockedBy"), this.getCriteria().getLockedBy())));
if (this.getCriteria().getTarget() != null)
query.where(((builder, root) -> builder.equal(root.get("target"), this.getCriteria().getTarget())));
return query;
}
@Override
public QueryableList<Lock> applyPaging(QueryableList<Lock> items) {
return PaginationService.applyPaging(items, this);
}
}

78
dmp-backend/data/src/main/java/eu/eudat/query/LockQuery.java Normal file
View File

@ -0,0 +1,78 @@
package eu.eudat.query;
import eu.eudat.data.dao.DatabaseAccessLayer;
import eu.eudat.data.entities.Lock;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.queryable.QueryableList;
import eu.eudat.queryable.types.FieldSelectionType;
import eu.eudat.queryable.types.SelectionField;
import javax.persistence.criteria.Subquery;
import java.util.Arrays;
import java.util.Date;
import java.util.List;
import java.util.UUID;
public class LockQuery extends Query<Lock, UUID> {
private UUID id;
private UUID target;
private UserQuery userQuery;
private Date touchedAt;
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public UUID getTarget() {
return target;
}
public void setTarget(UUID target) {
this.target = target;
}
public UserQuery getUserQuery() {
return userQuery;
}
public void setUserQuery(UserQuery userQuery) {
this.userQuery = userQuery;
}
public Date getTouchedAt() {
return touchedAt;
}
public void setTouchedAt(Date touchedAt) {
this.touchedAt = touchedAt;
}
public LockQuery(DatabaseAccessLayer<Lock, UUID> databaseAccessLayer, List<String> selectionFields) {
super(databaseAccessLayer, selectionFields);
}
public LockQuery(DatabaseAccessLayer<Lock, UUID> databaseAccessLayer) {
super(databaseAccessLayer);
}
@Override
public QueryableList<Lock> getQuery() {
QueryableList<Lock> query = this.databaseAccessLayer.asQueryable();
if (this.id != null) {
query.where((builder, root) -> builder.equal(root.get("id"), this.id));
}
if (this.target != null) {
query.where(((builder, root) -> builder.equal(root.get("target"), this.target)));
}
if (this.userQuery != null) {
Subquery<UserInfo> userSubQuery = this.userQuery.getQuery().query(Arrays.asList(new SelectionField(FieldSelectionType.FIELD, "id")));
query.where((builder, root) -> root.get("lockedBy").get("id").in(userSubQuery));
}
return query;
}
}

102
dmp-backend/elastic/src/main/java/eu/eudat/elastic/criteria/DatasetCriteria.java
View File

@ -3,12 +3,96 @@ package eu.eudat.elastic.criteria;
import eu.eudat.elastic.entities.Tag;
import java.util.List;
import java.util.UUID;
/**
* Created by ikalyvas on 7/5/2018.
*/
public class DatasetCriteria extends Criteria {
public List<Tag> tags;
private String like;
private List<UUID> datasetTemplates;
private Short status;
private List<UUID> dmps;
private List<UUID> groupIds;
private List<UUID> grants;
private List<UUID> collaborators;
private Boolean allowAllVersions;
private List<String> organiztions;
private List<Tag> tags;
private boolean isPublic;
private Short grantStatus;
public String getLike() {
return like;
}
public void setLike(String like) {
this.like = like;
}
public List<UUID> getDatasetTemplates() {
return datasetTemplates;
}
public void setDatasetTemplates(List<UUID> datasetTemplates) {
this.datasetTemplates = datasetTemplates;
}
public Short getStatus() {
return status;
}
public void setStatus(Short status) {
this.status = status;
}
public List<UUID> getDmps() {
return dmps;
}
public void setDmps(List<UUID> dmps) {
this.dmps = dmps;
}
public List<UUID> getGroupIds() {
return groupIds;
}
public void setGroupIds(List<UUID> groupIds) {
this.groupIds = groupIds;
}
public List<UUID> getGrants() {
return grants;
}
public void setGrants(List<UUID> grants) {
this.grants = grants;
}
public List<UUID> getCollaborators() {
return collaborators;
}
public void setCollaborators(List<UUID> collaborators) {
this.collaborators = collaborators;
}
public Boolean getAllowAllVersions() {
return allowAllVersions;
}
public void setAllowAllVersions(Boolean allowAllVersions) {
this.allowAllVersions = allowAllVersions;
}
public List<String> getOrganiztions() {
return organiztions;
}
public void setOrganiztions(List<String> organiztions) {
this.organiztions = organiztions;
}
public List<Tag> getTags() {
return tags;
@ -17,4 +101,20 @@ public class DatasetCriteria extends Criteria {
public void setTags(List<Tag> tags) {
this.tags = tags;
}
public boolean isPublic() {
return isPublic;
}
public void setPublic(boolean aPublic) {
isPublic = aPublic;
}
public Short getGrantStatus() {
return grantStatus;
}
public void setGrantStatus(Short grantStatus) {
this.grantStatus = grantStatus;
}
}

44
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Collaborator.java Normal file
View File

@ -0,0 +1,44 @@
package eu.eudat.elastic.entities;
import org.elasticsearch.common.xcontent.XContentBuilder;
import java.io.IOException;
import java.util.Map;
import java.util.UUID;
public class Collaborator implements ElasticEntity<Collaborator> {
private String id;
private String name;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
@Override
public XContentBuilder toElasticEntity(XContentBuilder builder) throws IOException {
builder.startObject();
builder.field("id", this.id);
builder.field("name", this.name);
builder.endObject();
return builder;
}
@Override
public Collaborator fromElasticEntity(Map fields) {
this.id = (String) fields.get("id");
this.name = (String) fields.get("name");
return this;
}
}

230
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Dataset.java
View File

@ -5,9 +5,8 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.*;
import java.util.stream.Collectors;
/**
* Created by ikalyvas on 7/5/2018.
@ -15,8 +14,51 @@ import java.util.Map;
public class Dataset implements ElasticEntity<Dataset> {
private static final Logger logger = LoggerFactory.getLogger(Dataset.class);
public enum Status {
SAVED((short) 0), FINALISED((short) 1), CANCELED((short) 2), DELETED((short) 99),;
private short value;
private Status(short value) {
this.value = value;
}
public short getValue() {
return value;
}
public static Status fromInteger(int value) {
switch (value) {
case 0:
return SAVED;
case 1:
return FINALISED;
case 2:
return CANCELED;
case 99:
return DELETED;
default:
throw new RuntimeException("Unsupported Dataset Status");
}
}
}
private String id;
private List<Tag> tags = new LinkedList<>();
private String label;
private String description;
private UUID template;
private Short status;
private UUID dmp;
private UUID group;
private UUID grant;
private List<Collaborator> collaborators;
private Boolean lastVersion;
private Boolean lastPublicVersion;
private List<Organization> organizations;
private Boolean isPublic;
private Short grantStatus;
private String formData;
public String getId() {
return id;
@ -34,10 +76,158 @@ public class Dataset implements ElasticEntity<Dataset> {
this.tags = tags;
}
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public UUID getTemplate() {
return template;
}
public void setTemplate(UUID template) {
this.template = template;
}
public Short getStatus() {
return status;
}
public void setStatus(Short status) {
this.status = status;
}
public UUID getDmp() {
return dmp;
}
public void setDmp(UUID dmp) {
this.dmp = dmp;
}
public UUID getGroup() {
return group;
}
public void setGroup(UUID group) {
this.group = group;
}
public UUID getGrant() {
return grant;
}
public void setGrant(UUID grant) {
this.grant = grant;
}
public List<Collaborator> getCollaborators() {
return collaborators;
}
public void setCollaborators(List<Collaborator> collaborators) {
this.collaborators = collaborators;
}
public Boolean getLastVersion() {
return lastVersion;
}
public void setLastVersion(Boolean lastVersion) {
this.lastVersion = lastVersion;
}
public Boolean getLastPublicVersion() {
return lastPublicVersion;
}
public void setLastPublicVersion(Boolean lastPublicVersion) {
this.lastPublicVersion = lastPublicVersion;
}
public List<Organization> getOrganizations() {
return organizations;
}
public void setOrganizations(List<Organization> organizations) {
this.organizations = organizations;
}
public Boolean getPublic() {
return isPublic;
}
public void setPublic(Boolean aPublic) {
isPublic = aPublic;
}
public Short getGrantStatus() {
return grantStatus;
}
public void setGrantStatus(Short grantStatus) {
this.grantStatus = grantStatus;
}
public String getFormData() {
return formData;
}
public void setFormData(String formData) {
this.formData = formData;
}
@Override
public XContentBuilder toElasticEntity(XContentBuilder builder) throws IOException {
builder.startObject();
builder.field("id", this.id);
builder.field("label", this.label);
builder.field("description", this.description);
builder.field("template", this.template.toString());
builder.field("status", this.status.toString());
builder.field("dmp", this.dmp.toString());
if (this.group != null) {
builder.field("group", this.group.toString());
}
builder.field("grant", this.grant.toString());
if (collaborators != null) {
builder.startArray("collaborators");
this.collaborators.forEach(x -> {
try {
x.toElasticEntity(builder);
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
});
builder.endArray();
}
builder.field("lastVersion", this.lastVersion.toString());
builder.field("lastPublicVersion", this.lastPublicVersion.toString());
if (organizations != null) {
builder.startArray("organizations");
this.organizations.forEach(x -> {
try {
x.toElasticEntity(builder);
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
});
builder.endArray();
}
if (this.tags != null) {
builder.startArray("tags");
this.tags.forEach(x -> {
try {
@ -47,6 +237,14 @@ public class Dataset implements ElasticEntity<Dataset> {
}
});
builder.endArray();
}
if (this.isPublic != null) {
builder.field("public", this.isPublic.toString());
}
if (this.grantStatus != null) {
builder.field("grantStatus", this.grantStatus.toString());
}
builder.field("formData", this.formData);
builder.endObject();
return builder;
}
@ -55,7 +253,31 @@ public class Dataset implements ElasticEntity<Dataset> {
public Dataset fromElasticEntity(Map<String, Object> fields) {
if (fields != null) {
this.id = (String) fields.get("id");
this.tags = ((List<Tag>) fields.get("tags"));
if (fields.get("tags") != null) {
this.tags = ((List<HashMap>) fields.get("tags")).stream().map(hashMap -> new Tag().fromElasticEntity(hashMap)).collect(Collectors.toList());
}
this.label = (String) fields.get("label");
this.description = (String) fields.get("description");
this.template = UUID.fromString((String) fields.get("template"));
this.status = Short.valueOf((String) fields.get("status"));
this.dmp = UUID.fromString((String) fields.get("dmp"));
this.group = UUID.fromString((String) fields.get("group"));
this.grant = UUID.fromString((String) fields.get("grant"));
if (fields.get("collaborators") != null) {
this.collaborators = ((List<HashMap>) fields.get("collaborators")).stream().map(hashMap -> new Collaborator().fromElasticEntity(hashMap)).collect(Collectors.toList());
}
this.lastVersion = Boolean.parseBoolean((String) fields.get("lastVersion"));
this.lastPublicVersion = Boolean.parseBoolean((String) fields.get("lastPublicVersion"));
if (fields.get("organizations") != null) {
this.organizations = ((List<HashMap>) fields.get("organizations")).stream().map(hashMap -> new Organization().fromElasticEntity(hashMap)).collect(Collectors.toList());
}
if (fields.get("public") != null) {
this.isPublic = Boolean.valueOf((String) fields.get("public"));
}
if (fields.get("grantStatus") != null) {
this.grantStatus = Short.valueOf((String) fields.get("grantStatus"));
}
this.formData = (String) fields.get("formData");
}
return this;
}

43
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Organization.java Normal file
View File

@ -0,0 +1,43 @@
package eu.eudat.elastic.entities;
import org.elasticsearch.common.xcontent.XContentBuilder;
import java.io.IOException;
import java.util.Map;
public class Organization implements ElasticEntity<Organization> {
private String id;
private String name;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
@Override
public XContentBuilder toElasticEntity(XContentBuilder builder) throws IOException {
builder.startObject();
builder.field("id", this.id);
builder.field("name", this.name);
builder.endObject();
return builder;
}
@Override
public Organization fromElasticEntity(Map fields) {
this.id = (String) fields.get("id");
this.name = (String) fields.get("name");
return this;
}
}

6
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Tag.java
View File

@ -39,7 +39,9 @@ public class Tag implements ElasticEntity {
}
@Override
public Object fromElasticEntity(Map fields) {
return null;
public Tag fromElasticEntity(Map fields) {
this.id = (String) fields.get("id");
this.name = (String) fields.get("name");
return this;
}
}

113
dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/DatasetRepository.java
View File

@ -2,18 +2,22 @@ package eu.eudat.elastic.repository;
import eu.eudat.elastic.criteria.DatasetCriteria;
import eu.eudat.elastic.entities.Dataset;
import org.elasticsearch.action.admin.indices.get.GetIndexRequest;
import eu.eudat.elastic.entities.Tag;
import org.elasticsearch.action.get.GetRequest;
import org.elasticsearch.action.get.GetResponse;
import org.elasticsearch.action.index.IndexRequest;
import org.elasticsearch.action.search.SearchRequest;
import org.elasticsearch.action.search.SearchResponse;
import org.elasticsearch.action.search.SearchType;
import org.elasticsearch.client.RequestOptions;
import org.elasticsearch.client.RestHighLevelClient;
import org.elasticsearch.client.core.CountRequest;
import org.elasticsearch.client.core.CountResponse;
import org.elasticsearch.client.indices.GetIndexRequest;
import org.elasticsearch.common.xcontent.XContentBuilder;
import org.elasticsearch.common.xcontent.XContentFactory;
import org.elasticsearch.index.query.BoolQueryBuilder;
import org.elasticsearch.index.query.QueryBuilders;
import org.elasticsearch.index.reindex.DeleteByQueryRequest;
import org.elasticsearch.search.builder.SearchSourceBuilder;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
@ -21,12 +25,10 @@ import org.springframework.stereotype.Service;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.UUID;
import java.util.stream.Collectors;
import java.util.stream.Stream;
/**
* Created by ikalyvas on 7/5/2018.
*/
@Service("datasetRepository")
public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteria> {
@ -38,35 +40,110 @@ public class DatasetRepository extends ElasticRepository<Dataset, DatasetCriteri
@Override
public Dataset createOrUpdate(Dataset entity) throws IOException {
XContentBuilder builder = XContentFactory.jsonBuilder();
IndexRequest request = new IndexRequest("datasets", "doc", entity.getId()).source(entity.toElasticEntity(builder));
this.getClient().index(request);
IndexRequest request = new IndexRequest("datasets").id(entity.getId()).source(entity.toElasticEntity(builder));//new IndexRequest("datasets", "doc", entity.getId()).source(entity.toElasticEntity(builder));
this.getClient().index(request, RequestOptions.DEFAULT);
return entity;
}
@Override
public Dataset findDocument(String id) throws IOException {
GetRequest request = new GetRequest("datasets","doc",id);
GetResponse response = this.getClient().get(request);
GetRequest request = new GetRequest("datasets",id);
GetResponse response = this.getClient().get(request, RequestOptions.DEFAULT);
return new Dataset().fromElasticEntity(response.getSourceAsMap());
}
@Override
public List<Dataset> query(DatasetCriteria criteria) throws ExecutionException, InterruptedException, IOException {
SearchRequest searchRequest = new SearchRequest();
public List<Dataset> query(DatasetCriteria criteria) throws IOException {
SearchRequest searchRequest = new SearchRequest("datasets");
SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
BoolQueryBuilder boolQuery = QueryBuilders.boolQuery()
.should(QueryBuilders.termsQuery("tags.name.keyword", criteria.getTags().stream().map(x -> x.getName()).collect(Collectors.toList())));
CountRequest countRequest = new CountRequest("datasets");
countRequest.query(QueryBuilders.boolQuery().mustNot(QueryBuilders.termsQuery("status.keyword", Stream.of(Dataset.Status.DELETED.getValue(), Dataset.Status.CANCELED.getValue()).collect(Collectors.toList()))));
CountResponse countResponse = getClient().count(countRequest, RequestOptions.DEFAULT);
Long count = countResponse.getCount();
searchSourceBuilder.size(count.intValue());
BoolQueryBuilder boolQuery = QueryBuilders.boolQuery().mustNot(QueryBuilders.termsQuery("status.keyword", Stream.of(Dataset.Status.DELETED.getValue(), Dataset.Status.CANCELED.getValue()).collect(Collectors.toList())));
if (criteria.isPublic()) {
boolQuery = boolQuery.should(QueryBuilders.termQuery("public.keyword", "true"));
boolQuery = boolQuery.should(QueryBuilders.termQuery("status.keyword", Dataset.Status.FINALISED.getValue()));
boolQuery = boolQuery.should(QueryBuilders.termQuery("lastPublicVersion.keyword", "true"));
}
if (criteria.getLike() != null && !criteria.getLike().isEmpty()) {
boolQuery = boolQuery.should(QueryBuilders.queryStringQuery(criteria.getLike()).fields(Stream.of(new Object[][] {
{ "label", 1.0f },
{ "description", 1.0f },
{ "formData", 1.0f }
}).collect(Collectors.toMap(data -> (String) data[0], data -> (Float) data[1]))));
}
if (criteria.getDatasetTemplates() != null && criteria.getDatasetTemplates().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery("template.keyword", criteria.getDatasetTemplates().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getStatus() != null) {
boolQuery = boolQuery.should(QueryBuilders.termQuery("status.keyword", criteria.getStatus().toString()));
}
if (criteria.getDmps() != null && criteria.getDmps().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery("dmp.keyword", criteria.getDmps().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getGroupIds() != null && criteria.getGroupIds().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery("group.keyword", criteria.getGroupIds().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getGrants() != null && criteria.getGrants().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery("grant.keyword", criteria.getGrants().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (criteria.getGrantStatus() != null) {
boolQuery = boolQuery.should(QueryBuilders.termQuery("grantStatus.keyword", criteria.getGrantStatus().toString()));
}
if (criteria.getCollaborators() != null && criteria.getCollaborators().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery("collaborators.id.keyword", criteria.getCollaborators().stream().map(UUID::toString).collect(Collectors.toList())));
}
if (!criteria.isPublic()) {
if (criteria.getAllowAllVersions() != null && !criteria.getAllowAllVersions()) {
boolQuery = boolQuery.should(QueryBuilders.termQuery("lastVersion.keyword", "true"));
}
}
if (criteria.getOrganiztions() != null && criteria.getOrganiztions().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery("organizations.id.keyword", criteria.getOrganiztions()));
}
if (criteria.getTags() != null && criteria.getTags().size() > 0) {
boolQuery = boolQuery.should(QueryBuilders.termsQuery("tags.name.keyword", criteria.getTags().stream().map(Tag::getName).collect(Collectors.toList())));
}
if (boolQuery.should().isEmpty() && boolQuery.mustNot().isEmpty()) {
boolQuery.should(QueryBuilders.matchAllQuery());
} else {
boolQuery.minimumShouldMatch(boolQuery.should().size());
}
searchSourceBuilder.query(boolQuery);
searchRequest.source(searchSourceBuilder);
SearchResponse response = this.getClient().search(searchRequest);
SearchResponse response = this.getClient().search(searchRequest, RequestOptions.DEFAULT);
return Arrays.stream(response.getHits().getHits()).map(x -> this.transformFromString(x.getSourceAsString(), Dataset.class)).collect(Collectors.toList());
}
@Override
public boolean exists() throws IOException {
GetIndexRequest request = new GetIndexRequest();
request.indices("datasets");
return this.getClient().indices().exists(request);
GetIndexRequest request = new GetIndexRequest("datasets");
// request.indices("datasets");
return this.getClient().indices().exists(request, RequestOptions.DEFAULT);
}
@Override
public void clear() throws IOException {
if (exists()) {
DeleteByQueryRequest delete = new DeleteByQueryRequest("datasets");
delete.setQuery(QueryBuilders.matchAllQuery());
this.getClient().deleteByQuery(delete, RequestOptions.DEFAULT);
}
}
}

2
dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/Repository.java
View File

@ -19,4 +19,6 @@ public interface Repository<ET extends ElasticEntity, C extends Criteria> {
List<ET> query(C criteria) throws ExecutionException, InterruptedException, IOException;
boolean exists() throws IOException;
void clear() throws IOException;
}

5
dmp-backend/logging/target/maven-archiver/pom.properties
View File

@ -1,5 +0,0 @@
#Generated by Apache Maven
#Mon Jul 15 19:37:19 EEST 2019
version=1.0-SNAPSHOT
groupId=dmp-backend
artifactId=logging

14
dmp-backend/pom.xml
View File

@ -43,7 +43,7 @@
<slf4j.version>1.7.12</slf4j.version>
<jetty.version>9.0.7.v20131107
</jetty.version> <!-- Adapt this to a version found on http://repo.maven.apache.org/maven2/org/eclipse/jetty/jetty-maven-plugin/ -->
<logback.version>1.1.1</logback.version>
<logback.version>1.2.3</logback.version>
<javax.inject.version>1</javax.inject.version>
<javax.servlet.servlet-api.version>3.0.1</javax.servlet.servlet-api.version>
<docker.image.prefix>ikalyvas</docker.image.prefix>
@ -70,13 +70,13 @@
<dependency>
<groupId>org.elasticsearch</groupId>
<artifactId>elasticsearch</artifactId>
<version>6.3.1</version>
<version>7.6.0</version>
</dependency>
<dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>elasticsearch-rest-high-level-client</artifactId>
<version>6.3.1</version>
<version>7.6.0</version>
</dependency>
<dependency>
<groupId>org.hibernate</groupId>
@ -188,7 +188,13 @@
<dependency>
<groupId>org.elasticsearch.client</groupId>
<artifactId>transport</artifactId>
<version>6.3.0</version>
<version>7.6.0</version>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-to-slf4j</artifactId>
<version>2.8.2</version>
</dependency>
</dependencies>

21
dmp-backend/web/src/main/java/eu/eudat/configurations/ElasticSearchConfiguration.java
View File

@ -1,20 +1,17 @@
package eu.eudat.configurations;
import org.apache.http.HttpHost;
import org.elasticsearch.client.Client;
import org.apache.http.auth.AuthScope;
import org.apache.http.auth.UsernamePasswordCredentials;
import org.apache.http.client.CredentialsProvider;
import org.apache.http.impl.client.BasicCredentialsProvider;
import org.elasticsearch.client.RestClient;
import org.elasticsearch.client.RestHighLevelClient;
import org.elasticsearch.client.transport.TransportClient;
import org.elasticsearch.common.settings.Settings;
import org.elasticsearch.common.transport.TransportAddress;
import org.elasticsearch.transport.client.PreBuiltTransportClient;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.env.Environment;
import java.net.InetAddress;
/**
* Created by ikalyvas on 7/5/2018.
*/
@ -28,12 +25,18 @@ public class ElasticSearchConfiguration {
this.environment = environment;
}
@Bean
@Bean(destroyMethod = "close")
public RestHighLevelClient client() throws Exception {
final CredentialsProvider credentialsProvider = new BasicCredentialsProvider();
credentialsProvider.setCredentials(AuthScope.ANY,
new UsernamePasswordCredentials(this.environment.getProperty("elasticsearch.username"), this.environment.getProperty("elasticsearch.password")));
RestHighLevelClient client = new RestHighLevelClient(
RestClient.builder(
new HttpHost(this.environment.getProperty("elasticsearch.host"),
Integer.parseInt(this.environment.getProperty("elasticsearch.port")), "http")));
Integer.parseInt(this.environment.getProperty("elasticsearch.port")), "http"))
.setHttpClientConfigCallback(httpClientBuilder -> httpClientBuilder
.setDefaultCredentialsProvider(credentialsProvider)));
return client;
}
}

2
dmp-backend/web/src/main/java/eu/eudat/configurations/WebMVCConfiguration.java
View File

@ -7,6 +7,7 @@ import eu.eudat.logic.services.operations.authentication.AuthenticationService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Configuration;
import org.springframework.scheduling.annotation.EnableAsync;
import org.springframework.scheduling.annotation.EnableScheduling;
import org.springframework.web.method.support.HandlerMethodArgumentResolver;
import org.springframework.web.servlet.config.annotation.InterceptorRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurerAdapter;
@ -15,6 +16,7 @@ import java.util.List;
@EnableAsync
@Configuration
@EnableScheduling
public class WebMVCConfiguration extends WebMvcConfigurerAdapter {
private ApiContext apiContext;

14
dmp-backend/web/src/main/java/eu/eudat/controllers/DMPs.java
View File

@ -11,6 +11,7 @@ import eu.eudat.data.query.items.table.dmp.DataManagementPlanTableRequest;
import eu.eudat.data.query.items.table.dmp.DataManagmentPlanPublicTableRequest;
import eu.eudat.exceptions.datamanagementplan.DMPNewVersionException;
import eu.eudat.exceptions.datamanagementplan.DMPWithDatasetsDeleteException;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.managers.DataManagementPlanManager;
import eu.eudat.logic.managers.DatasetManager;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
@ -52,6 +53,9 @@ import java.util.List;
import java.util.Map;
import java.util.UUID;
import static org.springframework.http.MediaType.APPLICATION_ATOM_XML;
import static org.springframework.http.MediaType.APPLICATION_JSON;
@RestController
@CrossOrigin
@ -123,9 +127,13 @@ public class DMPs extends BaseController {
DataManagementPlanOverviewModel dataManagementPlan = this.dataManagementPlanManager.getOverviewSingle(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataManagementPlanOverviewModel>().status(ApiMessageCode.NO_MESSAGE).payload(dataManagementPlan));
} catch (Exception e) {
if (e instanceof UnauthorisedException) {
return ResponseEntity.status(HttpStatus.FORBIDDEN).body(new ResponseItem<DataManagementPlanOverviewModel>().status(ApiMessageCode.ERROR_MESSAGE));
} else {
return ResponseEntity.status(HttpStatus.NOT_FOUND).body(new ResponseItem<DataManagementPlanOverviewModel>().status(ApiMessageCode.ERROR_MESSAGE));
}
}
}
@RequestMapping(method = RequestMethod.GET, value = {"/public/{id}"})
public @ResponseBody
@ -219,8 +227,12 @@ public class DMPs extends BaseController {
}
@RequestMapping(method = RequestMethod.POST, value = {"/upload"})
public ResponseEntity<ResponseItem> dmpXmlUpload(@RequestParam("file") MultipartFile[] files, Principal principal) throws Exception {
public ResponseEntity<ResponseItem> dmpUpload(@RequestParam("file") MultipartFile[] files, Principal principal) throws Exception {
if (files[0].getContentType().equals(APPLICATION_JSON.toString())) {
this.dataManagementPlanManager.createFromRDA(files, principal);
} else if (files[0].getContentType().equals(APPLICATION_ATOM_XML.toString())) {
this.dataManagementPlanManager.createDmpFromXml(this.getApiContext(), files, principal);
}
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List>()
.status(ApiMessageCode.SUCCESS_MESSAGE));
}

3
dmp-backend/web/src/main/java/eu/eudat/controllers/DashBoardController.java
View File

@ -15,6 +15,7 @@ import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import java.io.IOException;
import java.util.List;
@RestController
@ -36,7 +37,7 @@ public class DashBoardController extends BaseController {
}
@RequestMapping(method = RequestMethod.GET, value = {"/dashboard/me/getStatistics"}, produces = "application/json")
public ResponseEntity<ResponseItem<DashBoardStatistics>> getStatistics(Principal principal) {
public ResponseEntity<ResponseItem<DashBoardStatistics>> getStatistics(Principal principal) throws IOException {
DashBoardStatistics statistics = dashBoardManager.getMeStatistics(principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DashBoardStatistics>().status(ApiMessageCode.NO_MESSAGE).payload(statistics));
}

36
dmp-backend/web/src/main/java/eu/eudat/controllers/DatasetWizardController.java
View File

@ -4,6 +4,7 @@ import eu.eudat.data.entities.Dataset;
import eu.eudat.data.query.items.item.dataset.DatasetWizardAutocompleteRequest;
import eu.eudat.data.query.items.item.datasetprofile.DatasetProfileWizardAutocompleteRequest;
import eu.eudat.exceptions.datasetwizard.DatasetWizardCannotUnlockException;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.managers.DatasetManager;
import eu.eudat.logic.managers.DatasetWizardManager;
import eu.eudat.logic.managers.UserManager;
@ -15,6 +16,7 @@ import eu.eudat.models.data.datasetwizard.DataManagentPlanListingModel;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.dmp.AssociatedProfile;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.listingmodels.DataManagementPlanOverviewModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.types.ApiMessageCode;
@ -30,6 +32,7 @@ import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.multipart.MultipartFile;
import javax.persistence.NoResultException;
import javax.transaction.Transactional;
import java.io.File;
import java.io.FileInputStream;
@ -79,13 +82,13 @@ public class DatasetWizardController extends BaseController {
@Transactional
@RequestMapping(method = RequestMethod.GET, value = {"{id}"}, produces = "application/json")
public @ResponseBody
ResponseEntity getSingle(@PathVariable String id, @RequestHeader("Content-Type") String contentType, @ClaimedAuthorities(claims = {ANONYMOUS}) Principal principal) throws IllegalAccessException, IOException, InstantiationException {
if(contentType.equals("application/xml")) {
ResponseEntity getSingle(@PathVariable String id, @RequestHeader("Content-Type") String contentType, Principal principal) throws IllegalAccessException, IOException, InstantiationException {
try {
if (contentType.equals("application/xml")) {
VisibilityRuleService visibilityRuleService = this.getApiContext().getUtilitiesService().getVisibilityRuleService();
return this.datasetManager.getDocument(id, visibilityRuleService, contentType);
}
else if (contentType.equals("application/msword")) {
File file = datasetManager.getWordDocument(this.configLoader, id, this.getApiContext().getUtilitiesService().getVisibilityRuleService());
return this.datasetManager.getDocument(id, visibilityRuleService, contentType, principal);
} else if (contentType.equals("application/msword")) {
File file = datasetManager.getWordDocumentFile(this.configLoader, id, this.getApiContext().getUtilitiesService().getVisibilityRuleService(), principal);
InputStream resource = new FileInputStream(file);
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(file.length());
@ -100,11 +103,22 @@ public class DatasetWizardController extends BaseController {
return new ResponseEntity<>(content,
responseHeaders,
HttpStatus.OK);
}
else {
DatasetWizardModel dataset = this.datasetManager.getSingle(id);
} else {
DatasetWizardModel dataset = this.datasetManager.getSingle(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DatasetWizardModel>().status(ApiMessageCode.NO_MESSAGE).payload(dataset));
}
} catch (Exception e) {
if (e instanceof UnauthorisedException) {
if (e instanceof UnauthorisedException) {
return ResponseEntity.status(HttpStatus.FORBIDDEN).body(new ResponseItem<DataManagementPlanOverviewModel>().status(ApiMessageCode.ERROR_MESSAGE));
} else if (e instanceof NoResultException) {
return ResponseEntity.status(HttpStatus.NOT_FOUND).body(new ResponseItem<DataManagementPlanOverviewModel>().status(ApiMessageCode.ERROR_MESSAGE));
} else {
throw e;
}
}
}
return null; // ????
}
@RequestMapping(method = RequestMethod.GET, value = {"/public/{id}"}, produces = "application/json")
@ -137,8 +151,8 @@ public class DatasetWizardController extends BaseController {
@RequestMapping(method = RequestMethod.GET, value = {"/getPDF/{id}"})
public @ResponseBody
ResponseEntity<byte[]> getPDFDocument(@PathVariable String id) throws IllegalAccessException, IOException, InstantiationException, InterruptedException {
File file = datasetManager.getWordDocument(this.configLoader, id, this.getApiContext().getUtilitiesService().getVisibilityRuleService());
ResponseEntity<byte[]> getPDFDocument(@PathVariable String id, Principal principal) throws IllegalAccessException, IOException, InstantiationException, InterruptedException {
File file = datasetManager.getWordDocumentFile(this.configLoader, id, this.getApiContext().getUtilitiesService().getVisibilityRuleService(), principal);
String fileName = file.getName();
if (fileName.endsWith(".docx")){
fileName = fileName.substring(0, fileName.length() - 5);

18
dmp-backend/web/src/main/java/eu/eudat/controllers/Datasets.java
View File

@ -39,7 +39,7 @@ public class Datasets extends BaseController {
@RequestMapping(method = RequestMethod.POST, value = {"paged"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DataTableData<DatasetListingModel>>> getPaged(@RequestBody DatasetTableRequest datasetTableRequest, Principal principal) throws Exception {
ResponseEntity<ResponseItem<DataTableData<DatasetListingModel>>> getPaged(@RequestBody DatasetTableRequest datasetTableRequest, @ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) throws Exception {
DataTableData<DatasetListingModel> dataTable = this.datasetManager.getPaged(datasetTableRequest, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataTableData<DatasetListingModel>>().status(ApiMessageCode.NO_MESSAGE).payload(dataTable));
}
@ -66,5 +66,21 @@ public class Datasets extends BaseController {
DataTableData<DatasetProfileListingModel> datasetProfileTableData = this.datasetManager.getDatasetProfilesUsedByDatasets(datasetProfileTableRequestItem, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataTableData<DatasetProfileListingModel>>().status(ApiMessageCode.NO_MESSAGE).payload(datasetProfileTableData));
}
@javax.transaction.Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/index"})
public @ResponseBody
ResponseEntity<ResponseItem<Dataset>> generateIndex(Principal principal) throws Exception {
this.datasetManager.generateIndex(principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<eu.eudat.data.entities.Dataset>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Generated").payload(null));
}
@javax.transaction.Transactional
@RequestMapping(method = RequestMethod.DELETE, value = {"/index"})
public @ResponseBody
ResponseEntity<ResponseItem<Dataset>> clearIndex(Principal principal) throws Exception {
this.datasetManager.clearIndex(principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<eu.eudat.data.entities.Dataset>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Cleared").payload(null));
}
}

2
dmp-backend/web/src/main/java/eu/eudat/controllers/LanguageController.java
View File

@ -19,7 +19,7 @@ import java.util.UUID;
@RequestMapping(value = {"/api/language/"})
public class LanguageController {
Environment environment;
private Environment environment;
@Autowired
public LanguageController(Environment environment) {

56
dmp-backend/web/src/main/java/eu/eudat/controllers/LockController.java Normal file
View File

@ -0,0 +1,56 @@
package eu.eudat.controllers;
import com.sun.org.apache.xpath.internal.operations.Bool;
import eu.eudat.logic.managers.LockManager;
import eu.eudat.models.data.dmp.DataManagementPlan;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.lock.Lock;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.*;
import java.util.UUID;
@RestController
@CrossOrigin
@RequestMapping(value = {"/api/lock/"})
public class LockController {
private LockManager lockManager;
@Autowired
public LockController(LockManager lockManager) {
this.lockManager = lockManager;
}
@Transactional
@RequestMapping(method = RequestMethod.GET, path = "target/status/{id}")
public @ResponseBody ResponseEntity<ResponseItem<Boolean>> getLocked(@PathVariable String id, Principal principal) throws Exception {
boolean locked = this.lockManager.isLocked(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Boolean>().status(ApiMessageCode.SUCCESS_MESSAGE).message("locked").payload(locked));
}
@Transactional
@RequestMapping(method = RequestMethod.DELETE, path = "target/unlock/{id}")
public @ResponseBody ResponseEntity<ResponseItem<String>> unlock(@PathVariable String id, Principal principal) throws Exception {
this.lockManager.unlock(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created").payload("Lock Removed"));
}
@Transactional
@RequestMapping(method = RequestMethod.POST, consumes = "application/json", produces = "application/json")
public @ResponseBody ResponseEntity<ResponseItem<UUID>> createOrUpdate(@RequestBody Lock lock, Principal principal) throws Exception {
eu.eudat.data.entities.Lock result = this.lockManager.createOrUpdate(lock, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<UUID>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Created").payload(result.getId()));
}
@RequestMapping(method = RequestMethod.GET, path = "target/{id}")
public @ResponseBody ResponseEntity<ResponseItem<Lock>> getSingle(@PathVariable String id, Principal principal) throws Exception {
Lock lock = this.lockManager.getFromTarget(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Lock>().status(ApiMessageCode.NO_MESSAGE).payload(lock));
}
}

28
dmp-backend/web/src/main/java/eu/eudat/controllers/TagController.java
View File

@ -1,30 +1,27 @@
package eu.eudat.controllers;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.elastic.criteria.DatasetCriteria;
import eu.eudat.elastic.criteria.TagCriteria;
import eu.eudat.elastic.entities.Dataset;
import eu.eudat.elastic.entities.Tag;
import eu.eudat.elastic.repository.Repository;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.external.TagExternalSourcesModel;
import eu.eudat.logic.utilities.helpers.StreamDistinctBy;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.types.ApiMessageCode;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.*;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ExecutionException;
import java.util.stream.Collectors;
/**
* Created by ikalyvas on 7/5/2018.
@ -46,12 +43,13 @@ public class TagController extends BaseController {
@RequestMapping(method = RequestMethod.GET, value = {"/external/tags"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<TagExternalSourcesModel>> listExternalTagModel(
@RequestParam(value = "query", required = false) String query, @RequestParam(value = "type", required = false) String type) throws HugeResultSet, NoURLFound, IOException {
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
List<Map<String, String>> remoteRepos = this.getApiContext().getOperationsContext().getRemoteFetcher().getTags(externalUrlCriteria, type);
TagExternalSourcesModel researchersExternalSourcesModel = new TagExternalSourcesModel().fromExternalItem(remoteRepos);
ResponseEntity<ResponseItem<List<Tag>>> listExternalTagModel(
@RequestParam(value = "query", required = false) String query, @RequestParam(value = "type", required = false) String type) throws HugeResultSet, NoURLFound, IOException, ExecutionException, InterruptedException {
//ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
/*List<Map<String, String>> remoteRepos = this.getApiContext().getOperationsContext().getRemoteFetcher().getTags(externalUrlCriteria, type);
TagExternalSourcesModel researchersExternalSourcesModel = new TagExternalSourcesModel().fromExternalItem(remoteRepos);*/
List<Tag> tags = this.getApiContext().getOperationsContext().getDatasetRepository().query(new DatasetCriteria()).stream().map(Dataset::getTags).flatMap(Collection::stream).filter(StreamDistinctBy.distinctByKey(Tag::getId)).collect(Collectors.toList());
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<TagExternalSourcesModel>().payload(researchersExternalSourcesModel).status(ApiMessageCode.NO_MESSAGE));
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Tag>>().payload(tags).status(ApiMessageCode.NO_MESSAGE));
}
}

70
dmp-backend/web/src/main/java/eu/eudat/controllers/UserGuideController.java Normal file
View File

@ -0,0 +1,70 @@
package eu.eudat.controllers;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.userguide.UserGuide;
import eu.eudat.types.ApiMessageCode;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import java.io.*;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@RestController
@CrossOrigin
@RequestMapping(value = {"/api/userguide/"})
public class UserGuideController {
private Environment environment;
@Autowired
public UserGuideController(Environment environment) {
this.environment = environment;
}
@RequestMapping(path = "current", method = RequestMethod.GET )
public ResponseEntity getUserGuide() throws IOException {
Stream<Path> walk = Files.walk(Paths.get(this.environment.getProperty("userguide.path")));
List<String> result = walk.filter(Files::isRegularFile)
.map(Path::toString).collect(Collectors.toList());
String fileName = result.get(0);
InputStream is = new FileInputStream(fileName);
String[] filepath = fileName.split("\\.")[0].split("\\\\");
String simplename = filepath[filepath.length - 1];
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(is.available());
responseHeaders.setContentType(MediaType.TEXT_HTML);
responseHeaders.set("Content-Disposition", "attachment;filename=" + simplename);
responseHeaders.set("Access-Control-Expose-Headers", "Content-Disposition");
responseHeaders.get("Access-Control-Expose-Headers").add("Content-Type");
byte[] content = new byte[is.available()];
is.read(content);
is.close();
return new ResponseEntity<>(content, responseHeaders, HttpStatus.OK);
}
@RequestMapping(value = "current", method = RequestMethod.POST)
public @ResponseBody
ResponseEntity<ResponseItem<String>> updateGuide(@RequestBody UserGuide guide) throws Exception {
String fileName = this.environment.getProperty("userguide.path") + guide.getName() + ".html";
OutputStream os = new FileOutputStream(fileName);
os.write(guide.getHtml().getBytes());
os.close();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Updated").payload("Updated"));
}
}

50
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DashBoardManager.java
View File

@ -1,14 +1,12 @@
package eu.eudat.logic.managers;
import eu.eudat.data.dao.criteria.DataManagementPlanCriteria;
import eu.eudat.data.dao.criteria.DatasetCriteria;
import eu.eudat.data.dao.criteria.OrganisationCriteria;
import eu.eudat.data.dao.criteria.GrantCriteria;
import eu.eudat.data.dao.criteria.*;
import eu.eudat.data.dao.entities.DMPDao;
import eu.eudat.data.dao.entities.DatasetDao;
import eu.eudat.data.dao.entities.OrganisationDao;
import eu.eudat.data.dao.entities.GrantDao;
import eu.eudat.data.entities.*;
import eu.eudat.data.query.items.table.dmp.DataManagmentPlanPublicTableRequest;
import eu.eudat.logic.builders.model.models.RecentActivityDataBuilder;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
@ -18,15 +16,21 @@ import eu.eudat.models.data.dashboard.searchbar.SearchBarItem;
import eu.eudat.models.data.dashboard.statistics.DashBoardStatistics;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.searchbar.SearchBarItemType;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import java.io.IOException;
import java.util.LinkedList;
import java.util.List;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;
@Component
public class DashBoardManager {
private static final Logger logger = LoggerFactory.getLogger(DashBoardManager.class);
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
@ -40,13 +44,25 @@ public class DashBoardManager {
public DashBoardStatistics getStatistics() {
DashBoardStatistics statistics = new DashBoardStatistics();
DataManagementPlanCriteria dataManagementPlanCriteria = new DataManagementPlanCriteria();
DataManagmentPlanPublicTableRequest publicTableRequest = new DataManagmentPlanPublicTableRequest();
DataManagementPlanPublicCriteria publicCriteria = new DataManagementPlanPublicCriteria();
publicCriteria.setAllVersions(false);
publicTableRequest.setCriteria(publicCriteria);
publicTableRequest.setQuery(databaseRepository.getDmpDao().asQueryable());
List<DMP> dmps = publicTableRequest.applyCriteria().toList();
// DataManagementPlanCriteria dataManagementPlanCriteria = new DataManagementPlanCriteria();
OrganisationCriteria organisationCriteria = new OrganisationCriteria();
dataManagementPlanCriteria.setAllVersions(false);
dataManagementPlanCriteria.setIsPublic(true);
/*dataManagementPlanCriteria.setAllVersions(false);
dataManagementPlanCriteria.setIsPublic(true);*/
organisationCriteria.setPublic(true);
List<DMP> dmps = databaseRepository.getDmpDao().getWithCriteria(dataManagementPlanCriteria).toList();
// List<DMP> dmps = databaseRepository.getDmpDao().getWithCriteria(dataManagementPlanCriteria).toList();
long numberOfDatasets = 0;
LinkedList<Grant> grants = new LinkedList<>();
for (DMP dmp : dmps) {
@ -63,7 +79,8 @@ public class DashBoardManager {
return statistics;
}
public DashBoardStatistics getMeStatistics(Principal principal) {
public DashBoardStatistics getMeStatistics(Principal principal) throws IOException {
List<eu.eudat.elastic.entities.Dataset> datasets = null;
DashBoardStatistics statistics = new DashBoardStatistics();
DMPDao dataManagementPlanRepository = databaseRepository.getDmpDao();
DatasetDao datasetRepository = databaseRepository.getDatasetDao();
@ -72,7 +89,19 @@ public class DashBoardManager {
UserInfo user = new UserInfo();
user.setId(principal.getId());
DatasetCriteria datasetCriteria = new DatasetCriteria();
if (apiContext.getOperationsContext().getDatasetRepository() != null) {
try {
eu.eudat.elastic.criteria.DatasetCriteria datasetElasticCriteria = new eu.eudat.elastic.criteria.DatasetCriteria();
datasetElasticCriteria.setAllowAllVersions(false);
datasetElasticCriteria.setPublic(false);
datasets = apiContext.getOperationsContext().getDatasetRepository().query(datasetElasticCriteria);
}catch (Exception e) {
logger.warn(e.getMessage(), e);
datasets = null;
}
}
datasetCriteria.setAllVersions(false);
datasetCriteria.setIsPublic(false);
DataManagementPlanCriteria dataManagementPlanCriteria = new DataManagementPlanCriteria();
dataManagementPlanCriteria.setAllVersions(false);
GrantCriteria grantCriteria = new GrantCriteria();
@ -80,7 +109,8 @@ public class DashBoardManager {
List<Integer> roles = new LinkedList<>();
CompletableFuture dmpFuture = dataManagementPlanRepository.getAuthenticated(dataManagementPlanRepository.getWithCriteria(dataManagementPlanCriteria), principal.getId(), roles).countAsync()
.whenComplete((dmpsStats, throwable) -> statistics.setTotalDataManagementPlanCount(dmpsStats));
CompletableFuture datasetFuture = datasetRepository.getAuthenticated(datasetRepository.getWithCriteria(datasetCriteria), user, roles).countAsync()
List<eu.eudat.elastic.entities.Dataset> finalDatasets = datasets;
CompletableFuture datasetFuture = datasetRepository.getAuthenticated(datasets != null ? datasetRepository.asQueryable().where((builder, root) -> root.get("id").in(finalDatasets.stream().map(x -> UUID.fromString(x.getId())).collect(Collectors.toList()))) : datasetRepository.getWithCriteria(datasetCriteria), user, roles).countAsync()
.whenComplete((datasetsStats, throwable) -> statistics.setTotalDataSetCount(datasetsStats));
CompletableFuture grantFuture = grantRepository.getAuthenticated(grantRepository.getWithCriteria(grantCriteria), user).countAsync()
.whenComplete((grantsStats, throwable) -> statistics.setTotalGrantCount(grantsStats));

404
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java
View File

@ -1,6 +1,7 @@
package eu.eudat.logic.managers;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.configurations.dynamicgrant.DynamicGrantConfiguration;
import eu.eudat.configurations.dynamicgrant.entities.Property;
@ -9,10 +10,16 @@ import eu.eudat.data.dao.entities.*;
import eu.eudat.data.entities.Organisation;
import eu.eudat.data.entities.Researcher;
import eu.eudat.data.entities.*;
import eu.eudat.data.enumeration.notification.ActiveStatus;
import eu.eudat.data.enumeration.notification.ContactType;
import eu.eudat.data.enumeration.notification.NotificationType;
import eu.eudat.data.enumeration.notification.NotifyState;
import eu.eudat.data.query.items.item.dmp.DataManagementPlanCriteriaRequest;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
import eu.eudat.data.query.items.table.dmp.DataManagementPlanTableRequest;
import eu.eudat.data.query.items.table.dmp.DataManagmentPlanPublicTableRequest;
import eu.eudat.elastic.entities.Collaborator;
import eu.eudat.elastic.entities.Organization;
import eu.eudat.exceptions.datamanagementplan.DMPNewVersionException;
import eu.eudat.exceptions.datamanagementplan.DMPWithDatasetsDeleteException;
import eu.eudat.exceptions.security.UnauthorisedException;
@ -35,12 +42,15 @@ import eu.eudat.models.data.dmp.*;
import eu.eudat.models.data.dynamicfields.DynamicFieldWithValue;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.DataManagementPlanProfile;
import eu.eudat.models.data.entities.xmlmodels.dmpprofiledefinition.Field;
import eu.eudat.models.data.funder.FunderDMPEditorModel;
import eu.eudat.models.data.grant.GrantDMPEditorModel;
import eu.eudat.models.data.helpermodels.Tuple;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.listingmodels.DataManagementPlanListingModel;
import eu.eudat.models.data.listingmodels.DataManagementPlanOverviewModel;
import eu.eudat.models.data.listingmodels.DatasetListingModel;
import eu.eudat.models.data.listingmodels.UserInfoListingModel;
import eu.eudat.models.data.project.ProjectDMPEditorModel;
import eu.eudat.models.data.rda.RDAExportModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
@ -59,6 +69,8 @@ import org.springframework.http.*;
import org.springframework.stereotype.Component;
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.util.MultiValueMap;
import org.springframework.web.client.HttpClientErrorException;
import org.springframework.web.client.HttpServerErrorException;
import org.springframework.web.client.RestTemplate;
import org.springframework.web.multipart.MultipartFile;
import org.w3c.dom.Document;
@ -75,24 +87,34 @@ import java.nio.file.Files;
import java.util.*;
import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@Component
public class DataManagementPlanManager {
private static final Logger logger = LoggerFactory.getLogger(DataManagementPlanManager.class);
private final Map<NotificationType, String> notificationPaths = Stream.of(new Object[][] {
{NotificationType.DMP_MODIFIED, "/plans/edit"},
{NotificationType.DMP_PUBLISH, "/plans/publicEdit"},
{NotificationType.DMP_FINALISED, "/plans/edit"},
{NotificationType.DMP_MODIFIED_FINALISED, "/plans/edit"}
}).collect(Collectors.toMap(data -> (NotificationType) data[0], data -> (String) data[1]));
private ApiContext apiContext;
private DatasetManager datasetManager;
private UtilitiesService utilitiesService;
private DatabaseRepository databaseRepository;
private Environment environment;
private RDAManager rdaManager;
@Autowired
public DataManagementPlanManager(ApiContext apiContext, DatasetManager datasetManager, Environment environment) {
public DataManagementPlanManager(ApiContext apiContext, DatasetManager datasetManager, Environment environment, RDAManager rdaManager) {
this.apiContext = apiContext;
this.datasetManager = datasetManager;
this.utilitiesService = apiContext.getUtilitiesService();
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.environment = environment;
this.rdaManager = rdaManager;
}
public DataTableData<DataManagementPlanListingModel> getPaged(DataManagementPlanTableRequest dataManagementPlanTableRequest, Principal principal, String fieldsGroup) throws Exception {
@ -180,6 +202,10 @@ public class DataManagementPlanManager {
}
public File getWordDocument(String id, Principal principal, ConfigLoader configLoader) throws IOException {
return this.getWordDocument(id, principal, configLoader, false);
}
public File getWordDocument(String id, Principal principal, ConfigLoader configLoader, Boolean versioned) throws IOException {
WordBuilder wordBuilder = new WordBuilder();
VisibilityRuleService visibilityRuleService = this.utilitiesService.getVisibilityRuleService();
DatasetWizardModel dataset = new DatasetWizardModel();
@ -325,9 +351,14 @@ public class DataManagementPlanManager {
document.removeBodyElement(0);
}
String fileName = dmpEntity.getLabel();
String fileName = "";
if (versioned) {
fileName = dmpEntity.getLabel() + " v" + dmpEntity.getVersion();
} else {
fileName = dmpEntity.getLabel();
}
fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
File exportFile = new File(fileName + ".docx");
File exportFile = new File(this.environment.getProperty("temp.temp") + fileName + ".docx");
FileOutputStream out = new FileOutputStream(exportFile);
document.write(out);
out.close();
@ -474,13 +505,16 @@ public class DataManagementPlanManager {
}
public DMP createOrUpdate(ApiContext apiContext, DataManagementPlanEditorModel dataManagementPlan, Principal principal) throws Exception {
boolean setNotification = false;
if (dataManagementPlan.getId() != null) {
DMP dmp1 = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(dataManagementPlan.getId());
if (!isUserOwnerOfDmp(dmp1, principal)) {
throw new Exception("User not being the creator is not authorized to edit this DMP.");
}
if (dmp1.getModified().getTime() != dataManagementPlan.getModified().getTime()) {
throw new Exception("Another user have already edit that DMP.");
}
List<Dataset> datasetList = new ArrayList<>(dmp1.getDataset());
for (Dataset dataset : datasetList) {
if (dataManagementPlan.getProfiles().stream().filter(associatedProfile -> dataset.getProfile().getId().equals(associatedProfile.getId())).findAny().orElse(null) == null)
@ -488,6 +522,8 @@ public class DataManagementPlanManager {
}
if (dataManagementPlan.getStatus() == (int) DMP.DMPStatus.FINALISED.getValue() && dmp1.getStatus().equals(DMP.DMPStatus.FINALISED.getValue()))
throw new Exception("DMP is finalized, therefore cannot be edited.");
setNotification = true;
}
DMP newDmp = dataManagementPlan.toDataModel();
@ -565,9 +601,41 @@ public class DataManagementPlanManager {
if (dataManagementPlan.getAssociatedUsers().size() == 0)
assignUser(newDmp, user);
if (setNotification) {
if (newDmp.getStatus() != DMP.DMPStatus.FINALISED.getValue()) {
this.sendNotification(newDmp, user, NotificationType.DMP_MODIFIED);
} else {
this.sendNotification(newDmp, user, NotificationType.DMP_MODIFIED_FINALISED);
}
}
return newDmp;
}
private void sendNotification(DMP dmp, UserInfo user, NotificationType notificationType) {
List<UserDMP> userDMPS = databaseRepository.getUserDmpDao().asQueryable().where(((builder, root) -> builder.equal(root.get("dmp").get("id"), dmp.getId()))).toList();
for (UserDMP userDMP : userDMPS) {
if (!userDMP.getUser().getId().equals(user.getId())) {
Notification notification = new Notification();
notification.setUserId(user);
notification.setType(notificationType);
notification.setNotifyState(NotifyState.PENDING);
notification.setIsActive(ActiveStatus.ACTIVE);
notification.setData("{" +
"\"userId\": \"" + userDMP.getUser().getId() + "\"" +
", \"id\": \"" + userDMP.getDmp().getId() + "\"" +
", \"name\": \"" + userDMP.getDmp().getLabel() + "\"" +
", \"path\": \"" + notificationPaths.get(notificationType) +"\"" +
"}");
notification.setCreatedAt(new Date());
notification.setUpdatedAt(notification.getCreatedAt());
notification.setContactTypeHint(ContactType.EMAIL);
notification.setContactHint(userDMP.getUser().getEmail());
databaseRepository.getNotificationDao().createOrUpdate(notification);
}
}
}
private void assignUser(DMP dmp, UserInfo userInfo) {
UserDMP userDMP = new UserDMP();
@ -661,6 +729,21 @@ public class DataManagementPlanManager {
DMP oldDmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(uuid);
oldDmp.setStatus(DMP.DMPStatus.DELETED.getValue());
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(oldDmp);
DataManagementPlanCriteria criteria1 = new DataManagementPlanCriteria();
criteria1.setAllVersions(true);
criteria1.setGroupIds(Collections.singletonList(oldDmp.getGroupId()));
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(criteria1).toList().forEach(dmp -> {
for (Dataset dataset: dmp.getDataset()) {
try {
DatasetWizardModel datasetWizardModel = new DatasetWizardModel().fromDataModel(dataset);
datasetWizardModel.setTags(apiContext.getOperationsContext().getDatasetRepository().findDocument(dataset.getId().toString()).getTags());
datasetWizardModel.setDatasetProfileDefinition(this.datasetManager.getPagedProfile(datasetWizardModel, dataset));
this.datasetManager.updateTags(apiContext.getOperationsContext().getDatasetRepository(), datasetWizardModel);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
}
});
}
private void createResearchersIfTheyDontExist(DMP newDmp, ResearcherDao researcherRepository, UserInfo user) {
@ -694,8 +777,9 @@ public class DataManagementPlanManager {
if (newDmp.getGrant() != null) {
Grant grant = newDmp.getGrant();
GrantCriteria criteria = new GrantCriteria();
if (grant.getReference() != null) {
criteria.setReference(grant.getReference());
eu.eudat.data.entities.Grant grantEntity = grantDao.getWithCriteria(criteria).getSingleOrDefault();
eu.eudat.data.entities.Grant grantEntity = grantDao.getWithCriteria(criteria).toList().stream().max(Comparator.comparing(grant1 -> grant1.getModified().getTime())).orElse(null);
if (grantEntity != null) grant.setId(grantEntity.getId());
else {
grant.setType(Grant.GrantType.EXTERNAL.getValue());
@ -703,27 +787,39 @@ public class DataManagementPlanManager {
grantDao.createOrUpdate(grant);
}
}
else {
grant.setType(Grant.GrantType.EXTERNAL.getValue());
grant.setCreationUser(null);
grantDao.createOrUpdate(grant);
}
}
}
private void createFunderIfItDoesntExist(DMP newDmp, FunderDao funderDao) {
if (newDmp.getGrant().getFunder() != null) {
Funder funder = newDmp.getGrant().getFunder();
FunderCriteria criteria = new FunderCriteria();
if (funder.getReference() != null) {
criteria.setReference(funder.getReference());
eu.eudat.data.entities.Funder funderEntity = funderDao.getWithCritetia(criteria).getSingleOrDefault();
eu.eudat.data.entities.Funder funderEntity = funderDao.getWithCritetia(criteria).toList().stream().max(Comparator.comparing(funder1 -> funder1.getModified().getTime())).orElse(null);
if (funderEntity != null) funder.setId(funderEntity.getId());
else {
funderDao.createOrUpdate(funder);
}
}
else {
funderDao.createOrUpdate(funder);
}
}
}
private void createProjectIfItDoesntExist(DMP newDmp, ProjectDao projectDao) {
if (newDmp.getProject() != null) {
Project project = newDmp.getProject();
ProjectCriteria criteria = new ProjectCriteria();
if (project.getReference() != null) {
criteria.setReference(project.getReference());
eu.eudat.data.entities.Project projectEntity = projectDao.getWithCritetia(criteria).getSingleOrDefault();
eu.eudat.data.entities.Project projectEntity = projectDao.getWithCritetia(criteria).toList().stream().max(Comparator.comparing(project1 -> project1.getModified().getTime())).orElse(null);
if (projectEntity != null) project.setId(projectEntity.getId());
else {
project.setType(Project.ProjectType.EXTERNAL.getValue());
@ -731,6 +827,12 @@ public class DataManagementPlanManager {
projectDao.createOrUpdate(project);
}
}
else {
project.setType(Project.ProjectType.EXTERNAL.getValue());
if (project.getId() == null) project.setId(UUID.randomUUID());
projectDao.createOrUpdate(project);
}
}
}
private void checkIfUserCanEditGrant(DMP dmp, UserInfo user) throws Exception{
@ -761,19 +863,19 @@ public class DataManagementPlanManager {
}
private void assignGrandUserIfInternal(DMP dmp, UserInfo user) {
if (dmp.getGrant().getCreationUser() == null && dmp.getGrant().getReference().startsWith("dmp:")) {
if (dmp.getGrant().getCreationUser() == null && (dmp.getGrant().getReference() != null && dmp.getGrant().getReference().startsWith("dmp:"))) {
dmp.getGrant().setCreationUser(user);
}
}
private void assignFunderUserIfInternal(DMP dmp, UserInfo user) {
if (dmp.getGrant().getFunder().getCreationUser() == null && dmp.getGrant().getFunder().getReference().startsWith("dmp:")) {
if (dmp.getGrant().getFunder().getCreationUser() == null && ( dmp.getGrant().getFunder().getReference() != null && dmp.getGrant().getFunder().getReference().startsWith("dmp:"))) {
dmp.getGrant().getFunder().setCreationUser(user);
}
}
private void assignProjectUserIfInternal(DMP dmp, UserInfo user) {
if (dmp.getProject().getCreationUser() == null && dmp.getProject().getReference().startsWith("dmp:")) {
if (dmp.getProject().getCreationUser() == null && (dmp.getProject().getReference() != null && dmp.getProject().getReference().startsWith("dmp:"))) {
dmp.getProject().setCreationUser(user);
}
}
@ -784,6 +886,14 @@ public class DataManagementPlanManager {
datasetDao.asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class)).where((builder, root) -> builder.equal(root.get("id"), dataset.getId())).getSingleAsync()
.thenApplyAsync(entityDataset -> {
Dataset newDataset = new Dataset();
try {
DatasetWizardModel datasetWizardModel = new DatasetWizardModel().fromDataModel(entityDataset);
datasetWizardModel.setTags(apiContext.getOperationsContext().getDatasetRepository().findDocument(dataset.getId().toString()).getTags());
datasetWizardModel.setDatasetProfileDefinition(this.datasetManager.getPagedProfile(datasetWizardModel, entityDataset));
this.datasetManager.updateTags(apiContext.getOperationsContext().getDatasetRepository(), datasetWizardModel);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
newDataset.update(entityDataset);
newDataset.setDmp(newDmp);
newDataset.setStatus(Dataset.Status.SAVED.getValue());
@ -834,7 +944,48 @@ public class DataManagementPlanManager {
newDataset.setCreated(new Date());
return newDataset;
}).thenApplyAsync(item -> {
futures.add(datasetDao.createOrUpdateAsync(item));
futures.add(datasetDao.createOrUpdateAsync(item).whenComplete(((dataset1, throwable) -> {
eu.eudat.elastic.entities.Dataset datasetElastic = new eu.eudat.elastic.entities.Dataset();
datasetElastic.setId(dataset1.getId().toString());
datasetElastic.setLabel(dataset1.getLabel());
datasetElastic.setDescription(dataset1.getDescription());
datasetElastic.setTemplate(dataset1.getProfile().getId());
datasetElastic.setStatus(dataset1.getStatus());
datasetElastic.setDmp(dataset1.getDmp().getId());
datasetElastic.setGroup(dataset1.getDmp().getGroupId());
datasetElastic.setGrant(dataset1.getDmp().getGrant().getId());
if (dataset1.getDmp().getUsers() != null) {
datasetElastic.setCollaborators(dataset1.getDmp().getUsers().stream().map(user -> {
Collaborator collaborator = new Collaborator();
collaborator.setId(user.getId().toString());
// collaborator.setName(user.getUser().getName());
return collaborator;
}).collect(Collectors.toList()));
}
datasetElastic.setLastVersion(true);
datasetElastic.setLastPublicVersion(false);
if (dataset1.getDmp().getOrganisations() != null) {
datasetElastic.setOrganizations(dataset1.getDmp().getOrganisations().stream().map(org -> {
Organization organization = new Organization();
organization.setId(org.getId().toString());
organization.setName(org.getLabel());
return organization;
}).collect(Collectors.toList()));
}
datasetElastic.setPublic(dataset1.getDmp().isPublic());
datasetElastic.setGrantStatus(dataset1.getDmp().getGrant().getStatus());
try {
datasetElastic.setTags(apiContext.getOperationsContext().getDatasetRepository().findDocument(dataset.getId().toString()).getTags());
DatasetWizardModel datasetWizardModel = new DatasetWizardModel();
datasetWizardModel.setStatus(dataset1.getStatus());
datasetWizardModel.setDatasetProfileDefinition(this.datasetManager.getPagedProfile(datasetWizardModel, dataset1));
datasetElastic.setFormData(this.datasetManager.getWordDocumentText(datasetWizardModel));
apiContext.getOperationsContext().getDatasetRepository().createOrUpdate(datasetElastic);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
})));
return futures;
}).join();
@ -850,7 +1001,7 @@ public class DataManagementPlanManager {
List<Dataset> datasets = dmp.getDataset().stream().collect(Collectors.toList());
String fileName = dmp.getLabel();
fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
File xmlFile = new File(fileName + ".xml");
File xmlFile = new File(this.environment.getProperty("temp.temp") + fileName + ".xml");
BufferedWriter writer = new BufferedWriter(new FileWriter(xmlFile, true));
Document xmlDoc = XmlBuilder.getDocument();
Element dmpElement = xmlDoc.createElement("dmp");
@ -933,6 +1084,10 @@ public class DataManagementPlanManager {
for (Dataset dataset : datasets) {
Element datasetElement = xmlDoc.createElement("dataset");
Element datsetProfileElement = xmlDoc.createElement("profile");
datasetElement.setAttribute("name", dataset.getLabel());
datasetElement.appendChild(datsetProfileElement);
datsetProfileElement.setTextContent(dataset.getProfile().getId().toString());
DatasetWizardModel datasetWizardModel = new DatasetWizardModel();
Map<String, Object> properties = new HashMap<>();
@ -976,15 +1131,20 @@ public class DataManagementPlanManager {
eu.eudat.data.entities.DMP dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (!dmp.isPublic() && dmp.getUsers().stream().noneMatch(userInfo -> userInfo.getUser().getId() == principal.getId()))
throw new UnauthorisedException();
RDAExportModel rdaExportModel = new RDAExportModel().fromDataModel(dmp, datasetManager);
// RDAExportModel rdaExportModel = new RDAExportModel().fromDataModel(dmp, datasetManager, principal);
String result = rdaManager.convertToRDA(dmp);
ObjectMapper mapper = new ObjectMapper();
mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
String fileName = dmp.getLabel();
fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
File file = new File(fileName);
File file = new File(this.environment.getProperty("temp.temp") + fileName + ".json");
OutputStream output = new FileOutputStream(file);
try {
mapper.writeValue(file, rdaExportModel);
// mapper.writeValue(file, rdaExportModel);
output.write(result.getBytes());
output.flush();
output.close();
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
@ -1049,7 +1209,7 @@ public class DataManagementPlanManager {
// TODO Iterate through the list of dataManagementPlans.
// Creates new dataManagementPlan to fill it with the data model that was parsed from the xml.
// Creates properties.
DataManagementPlan dm = new DataManagementPlan();
DataManagementPlanEditorModel dm = new DataManagementPlanEditorModel();
DataManagementPlanProfile dmpProfile = new DataManagementPlanProfile();
List<Field> fieldList = new LinkedList<>();
@ -1063,12 +1223,29 @@ public class DataManagementPlanManager {
/*Tuple tuple = new Tuple();
tuple.setId(dataManagementPlans.get(0).getDmpProfile().getDmpProfileId());
tuple.setLabel(dataManagementPlans.get(0).getDmpProfile().getDmpProfileName());*/
eu.eudat.models.data.funder.Funder funder = new eu.eudat.models.data.funder.Funder();
FunderImportModels funderImport = dataManagementPlans.get(0).getFunderImportModels();
funder.setId(funderImport.getId());
funder.setLabel(funderImport.getLabel());
FunderDMPEditorModel funderEditor = new FunderDMPEditorModel();
funderEditor.setExistFunder(funder);
eu.eudat.models.data.grant.Grant grant = new eu.eudat.models.data.grant.Grant();
GrantImportModels grantImport = dataManagementPlans.get(0).getGrantImport();
grant.setId(grantImport.getId());
grant.setLabel(grantImport.getLabel());
grant.setAbbreviation(grantImport.getAbbreviation());
grant.setDescription(grantImport.getDescription());
GrantDMPEditorModel grantEditor = new GrantDMPEditorModel();
grantEditor.setExistGrant(grant);
eu.eudat.models.data.project.Project project = new eu.eudat.models.data.project.Project();
ProjectImportModels projectImport = dataManagementPlans.get(0).getProjectImportModels();
project.setId(projectImport.getId());
project.setLabel(projectImport.getLabel());
ProjectDMPEditorModel projectEditor = new ProjectDMPEditorModel();
projectEditor.setExistProject(project);
List<eu.eudat.models.data.dmp.AssociatedProfile> associatedProfiles = new LinkedList<>();
for (AssociatedProfileImportModels a : dataManagementPlans.get(0).getProfilesImportModels()) {
AssociatedProfile associatedProfile = new AssociatedProfile();
@ -1080,14 +1257,16 @@ public class DataManagementPlanManager {
for (OrganisationImportModel org : dataManagementPlans.get(0).getOrganisationImportModels()) {
eu.eudat.models.data.dmp.Organisation organisation = new eu.eudat.models.data.dmp.Organisation();
organisation.setLabel(org.getOrganaisationNameImport());
organisation.setId(org.getOrganaisationReferenceImport());
organisation.setReference(org.getOrganaisationReferenceImport());
organisation.setKey(organisation.getReference().split(":")[0]);
organisations.add(organisation);
}
List<eu.eudat.models.data.dmp.Researcher> researchers = new LinkedList<>();
for (ResearcherImportModels res : dataManagementPlans.get(0).getResearchersImportModels()) {
eu.eudat.models.data.dmp.Researcher researcher = new eu.eudat.models.data.dmp.Researcher();
researcher.setLabel(res.getResearcherImportName());
researcher.setId(res.getResearcherImportReference());
researcher.setReference(res.getResearcherImportReference());
researcher.setKey(researcher.getReference().split(":")[0]);
researchers.add(researcher);
}
@ -1096,7 +1275,9 @@ public class DataManagementPlanManager {
// Sets properties.
dm.setLabel(files[0].getOriginalFilename()); // Sets label.
dm.setGrant(grant); //Sets grant property.
dm.setGrant(grantEditor); //Sets grant property.
dm.setFunder(funderEditor);
dm.setProject(projectEditor);
dm.setDescription(dataManagementPlans.get(0).getDescriptionImport()); // Sets description property.
dm.setProfiles(associatedProfiles);
dm.setOrganisations(organisations); // Sets organisations property.
@ -1106,6 +1287,41 @@ public class DataManagementPlanManager {
dm.setDefinition(dmpProfile);
//createOrUpdate(apiContext, dm, principal);
DMP dmp = this.createOrUpdate(apiContext, dm, principal);
if (dmp.getOrganisations() == null) {
dmp.setOrganisations(new HashSet<>());
}
if (dmp.getResearchers() == null) {
dmp.setResearchers(new HashSet<>());
}
if (dmp.getDataset() == null) {
dmp.setDataset(new HashSet<>());
}
if (dmp.getUsers() == null) {
dmp.setUsers(new HashSet<>());
}
if (dmp.getAssociatedDmps() == null) {
dmp.setAssociatedDmps(new HashSet<>());
}
List<DatasetListingModel> datasets = new LinkedList<>();
for (DatasetImportModels das: dataManagementPlans.get(0).getDatasetImportModels()) {
eu.eudat.data.entities.Dataset dataset = new eu.eudat.data.entities.Dataset();
dataset.setLabel(das.getName());
dataset.setProfile(databaseRepository.getDatasetProfileDao().find(das.getProfile()));
dataset.setProperties(new ObjectMapper().writeValueAsString(das.getFieldImportModels()));
dataset.setStatus((short) 0);
dataset.setRegistries(new HashSet<>());
dataset.setDatasetDataRepositories(new HashSet<>());
dataset.setServices(new HashSet<>());
dataset.setDatasetExternalDatasets(new HashSet<>());
dataset.setDmp(dmp);
DatasetWizardModel datasetWizard = new DatasetWizardModel();
datasetWizard.setDatasetProfileDefinition(this.datasetManager.getPagedProfile(datasetWizard, dataset));
datasetWizard.fromDataModel(dataset);
this.datasetManager.createOrUpdate(datasetWizard, principal);
// datasets.add(new DatasetListingModel().fromDataModel(dataset));
}
logger.info(dm.toString());
}
@ -1113,6 +1329,62 @@ public class DataManagementPlanManager {
return dataManagementPlans;
}
public List<DMP> createFromRDA(MultipartFile[] files, Principal principal) throws IOException {
if (principal.getId() == null) {
throw new UnauthorisedException("No user is logged in");
}
List<DMP> result = new ArrayList<>();
for (MultipartFile file: files) {
DMP dmp = rdaManager.convertToEntity(new String(file.getBytes(), "UTF-8"));
dmp.setLabel(file.getOriginalFilename());
UserInfo me = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
dmp.setModified(new Date());
dmp.setCreator(me);
dmp.setVersion(0);
dmp.setStatus((short)0);
dmp.setGroupId(UUID.randomUUID());
if (dmp.getResearchers() != null && !dmp.getResearchers().isEmpty()) {
dmp.getResearchers().forEach(researcher -> {
researcher.setId(UUID.randomUUID());
researcher.setCreated(new Date());
researcher.setModified(new Date());
researcher.setStatus((short) 0);
apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao().createOrUpdate(researcher);
});
}
databaseRepository.getDmpDao().createOrUpdate(dmp);
assignUser(dmp, me);
dmp.getDataset().forEach(dataset -> {
dataset.setStatus(Dataset.Status.SAVED.getValue());
dataset.setCreated(new Date());
dataset.setModified(new Date());
dataset.setDmp(dmp);
dataset = databaseRepository.getDatasetDao().createOrUpdate(dataset);
dataset.setRegistries(new HashSet<>());
dataset.setDatasetDataRepositories(new HashSet<>());
dataset.setDatasetExternalDatasets(new HashSet<>());
dataset.setServices(new HashSet<>());
if (dmp.getOrganisations() == null) {
dmp.setOrganisations(new HashSet<>());
}
if (dmp.getResearchers() == null) {
dmp.setResearchers(new HashSet<>());
}
dmp.setUsers(new HashSet<>(apiContext.getOperationsContext().getDatabaseRepository().getUserDmpDao().asQueryable().where((builder, root) -> builder.equal(root.get("dmp").get("id"), dmp.getId())).toList()));
try {
DatasetWizardModel model = new DatasetWizardModel().fromDataModel(dataset);
model.setDatasetProfileDefinition(datasetManager.getPagedProfile(model, dataset));
datasetManager.updateTags(apiContext.getOperationsContext().getDatasetRepository(), model);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
});
result.add(dmp);
}
return result;
}
public DataTableData<DatasetProfileListingModel> getDatasetProfilesUsedByDMP(DatasetProfileTableRequestItem datasetProfileTableRequestItem, Principal principal) {
datasetProfileTableRequestItem.getCriteria().setFilter(DatasetProfileCriteria.DatasetProfileFilter.DMPs.getValue());
datasetProfileTableRequestItem.getCriteria().setUserId(principal.getId());
@ -1136,6 +1408,23 @@ public class DataManagementPlanManager {
throw new Exception("DMP is not finalized");
dmp.setPublic(true);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
criteria.setGroupIds(Collections.singletonList(dmp.getGroupId()));
criteria.setAllVersions(true);
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(criteria).toList().stream().forEach(dmp1 -> {
dmp1.getDataset().forEach(dataset -> {
try {
DatasetWizardModel datasetWizardModel = new DatasetWizardModel().fromDataModel(dataset);
datasetWizardModel.setTags(apiContext.getOperationsContext().getDatasetRepository().findDocument(dataset.getId().toString()).getTags());
datasetWizardModel.setDatasetProfileDefinition(this.datasetManager.getPagedProfile(datasetWizardModel, dataset));
this.datasetManager.updateTags(apiContext.getOperationsContext().getDatasetRepository(), datasetWizardModel);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
});
});
UserInfo user = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
sendNotification(dmp, user, NotificationType.DMP_PUBLISH);
}
public void makeFinalize(UUID id, Principal principal, DatasetsToBeFinalized datasetsToBeFinalized) throws Exception {
@ -1171,6 +1460,9 @@ public class DataManagementPlanManager {
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao()
.asQueryable().where((builder, root) -> root.get("id").in(datasetsToBeCanceled))
.update(root -> root.<Integer>get("status"), Dataset.Status.CANCELED.getValue());
UserInfo user = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(principal.getId());
sendNotification(dmp, user, NotificationType.DMP_FINALISED);
}
}
@ -1178,6 +1470,25 @@ public class DataManagementPlanManager {
return (dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getId()).equals(principal.getId());
}
private String getPreviousDOI(UUID groupId, UUID selfId) {
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
List<UUID> groupIds = new ArrayList<>();
groupIds.add(groupId);
criteria.setGroupIds(groupIds);
criteria.setAllVersions(true);
List<DMP> dmps = this.databaseRepository.getDmpDao().getWithCriteria(criteria).toList();
String doi = null;
for (DMP dmp: dmps) {
if (!dmp.getId().equals(selfId)) {
if (dmp.getDoi() != null && !dmp.getDoi().isEmpty()) {
doi = dmp.getDoi();
}
}
}
return doi;
}
public String createZenodoDoi(UUID id, Principal principal, ConfigLoader configLoader) throws Exception {
DMP dmp = this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(id);
if (!isUserOwnerOfDmp(dmp, principal))
@ -1190,22 +1501,63 @@ public class DataManagementPlanManager {
// First step, post call to Zenodo, to create the entry.
RestTemplate restTemplate = new RestTemplate();
HttpHeaders headers = new HttpHeaders();
headers.set("accept", "application/json");
headers.setAccept(Collections.singletonList(MediaType.APPLICATION_JSON));
headers.setContentType(MediaType.APPLICATION_JSON);
String createData = "{\n" +
" \"metadata\": {\n" +
" \"title\": \"" + dmp.getLabel() + "\",\n" +
" \"upload_type\": \"publication\",\n" +
" \"publication_type\": \"datamanagementplan\",\n" +
" \"description\": \"" + dmp.getDescription() + "\",\n" +
" \"description\": \"" + (dmp.getDescription() != null && !dmp.getDescription().isEmpty() ? dmp.getDescription() : "<p></p>") + "\",\n" +
" \"version\": \"" + dmp.getVersion() + "\",\n" +
" \"creators\": [{\n" +
" \t\t\"name\": \"" + dmp.getUsers().stream().filter(userDMP -> userDMP.getRole().equals(UserDMP.UserDMPRoles.OWNER.getValue())).findFirst().get().getUser().getName() + "\",\n" +
" \t\t\"affiliation\": \"OpenDMP\"}]\n" +
" }\n" +
"}";
HttpEntity<String> request = new HttpEntity<>(createData, headers);
JsonNode createDataJSON = new ObjectMapper().readTree(createData);
HttpEntity<JsonNode> request = new HttpEntity<>(createDataJSON, headers);
Map createResponse = null;
LinkedHashMap<String, String> links = null;
String previousDOI = this.getPreviousDOI(dmp.getGroupId(), dmp.getId());
try {
if (previousDOI == null) {
String createUrl = this.environment.getProperty("zenodo.url") + "deposit/depositions" + "?access_token=" + this.environment.getProperty("zenodo.access_token");
Map createResponse = restTemplate.postForObject(createUrl, request, Map.class);
createResponse = restTemplate.postForEntity(createUrl, request, Map.class).getBody();
links = (LinkedHashMap<String, String>) createResponse.get("links");
} else {
//It requires more than one step to create a new version
//First, get the deposit related to the concept DOI
String listUrl = this.environment.getProperty("zenodo.url") + "deposit/depositions" + "?q=conceptdoi:\"" + previousDOI + "\"&access_token=" + this.environment.getProperty("zenodo.access_token");
ResponseEntity<Map[]> listResponses = restTemplate.getForEntity(listUrl, Map[].class);
createResponse = listResponses.getBody()[0];
links = (LinkedHashMap<String, String>) createResponse.get("links");
//Second, make the new version (not in the links?)
String newVersionUrl = links.get("self") + "/actions/newversion" + "?access_token=" + this.environment.getProperty("zenodo.access_token");
createResponse = restTemplate.postForObject(newVersionUrl, null, Map.class);
links = (LinkedHashMap<String, String>) createResponse.get("links");
//Third, get the new deposit
String latestDraftUrl = links.get("latest_draft") + "?access_token=" + this.environment.getProperty("zenodo.access_token");
createResponse = restTemplate.getForObject(latestDraftUrl, Map.class);
links = (LinkedHashMap<String, String>) createResponse.get("links");
//At this point it might fail to perform the next requests so enclose them with try catch
try {
//Forth, update the new deposit's metadata
String updateUrl = links.get("self") + "?access_token=" + this.environment.getProperty("zenodo.access_token");
restTemplate.put(updateUrl, request);
//And finally remove pre-existing files from it
String fileListUrl = links.get("self") + "/files" + "?access_token=" + this.environment.getProperty("zenodo.access_token");
ResponseEntity<Map[]> fileListResponse = restTemplate.getForEntity(fileListUrl, Map[].class);
for (Map file : fileListResponse.getBody()) {
String fileDeleteUrl = links.get("self") + "/files/" + file.get("id") + "?access_token=" + this.environment.getProperty("zenodo.access_token");
restTemplate.delete(fileDeleteUrl);
}
}catch (Exception e) {
//In case the last two steps fail delete the latest Deposit it in order to create a new one (only one at a time is allowed)
restTemplate.delete(latestDraftUrl);
throw e;
}
}
// Second step, add the file to the entry.
HttpHeaders fileHeaders = new HttpHeaders();
@ -1218,7 +1570,6 @@ public class DataManagementPlanManager {
addFileMap.add("file", fileSystemResource);
HttpEntity<MultiValueMap<String, Object>> addFileMapRequest = new HttpEntity<>(addFileMap, fileHeaders);
LinkedHashMap<String, String> links = (LinkedHashMap<String, String>) createResponse.get("links");
String addFileUrl = links.get("files") + "?access_token=" + this.environment.getProperty("zenodo.access_token");
ResponseEntity<String> addFileResponse = restTemplate.postForEntity(addFileUrl, addFileMapRequest, String.class);
Files.deleteIfExists(file.toPath());
@ -1230,5 +1581,10 @@ public class DataManagementPlanManager {
dmp.setDoi((String) publishResponce.get("conceptdoi"));
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().createOrUpdate(dmp);
return (String) publishResponce.get("conceptdoi");
} catch (HttpClientErrorException | HttpServerErrorException ex) {
ObjectMapper ob = new ObjectMapper();
Map<String, String> parsedException = ob.readValue(ex.getResponseBodyAsString(), HashMap.class);
throw new IOException(parsedException.get("message"), ex);
}
}
}

347
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java
View File

@ -5,11 +5,19 @@ import eu.eudat.data.dao.entities.DataRepositoryDao;
import eu.eudat.data.dao.entities.DatasetDao;
import eu.eudat.data.dao.entities.RegistryDao;
import eu.eudat.data.entities.*;
import eu.eudat.data.enumeration.notification.ActiveStatus;
import eu.eudat.data.enumeration.notification.ContactType;
import eu.eudat.data.enumeration.notification.NotificationType;
import eu.eudat.data.enumeration.notification.NotifyState;
import eu.eudat.data.query.items.table.dataset.DatasetPublicTableRequest;
import eu.eudat.data.query.items.table.dataset.DatasetTableRequest;
import eu.eudat.data.query.items.table.datasetprofile.DatasetProfileTableRequestItem;
import eu.eudat.elastic.criteria.DatasetCriteria;
import eu.eudat.elastic.entities.Collaborator;
import eu.eudat.elastic.entities.Organization;
import eu.eudat.elastic.entities.Tag;
import eu.eudat.elastic.repository.DatasetRepository;
import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.logic.builders.BuilderFactory;
import eu.eudat.logic.builders.entity.UserInfoBuilder;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
@ -20,18 +28,22 @@ import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
import eu.eudat.logic.utilities.documents.types.ParagraphStyle;
import eu.eudat.logic.utilities.documents.word.WordBuilder;
import eu.eudat.logic.utilities.documents.xml.ExportXmlBuilder;
import eu.eudat.logic.utilities.helpers.StreamDistinctBy;
import eu.eudat.models.HintedModelFactory;
import eu.eudat.models.data.datasetImport.DatasetImportField;
import eu.eudat.models.data.datasetImport.DatasetImportPagedDatasetProfile;
import eu.eudat.models.data.datasetprofile.DatasetProfileListingModel;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.dmp.AssociatedProfile;
import eu.eudat.models.data.dmp.DataManagementPlan;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.listingmodels.DatasetListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.queryable.QueryableList;
import eu.eudat.types.Authorities;
import org.apache.commons.io.IOUtils;
import org.apache.poi.xwpf.extractor.XWPFWordExtractor;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.apache.poi.xwpf.usermodel.XWPFParagraph;
import org.apache.poi.xwpf.usermodel.XWPFRun;
@ -63,9 +75,7 @@ import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathFactory;
import java.io.*;
import java.math.BigInteger;
import java.net.URL;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.*;
import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;
@ -77,46 +87,100 @@ import java.util.zip.ZipInputStream;
public class DatasetManager {
private static final Logger logger = LoggerFactory.getLogger(DatasetManager.class);
private final Map<NotificationType, String> notificationPaths = Stream.of(new Object[][] {
{NotificationType.DATASET_MODIFIED, "/datasets/edit"},
{NotificationType.DATASET_MODIFIED_FINALISED, "/datasets/edit"}
}).collect(Collectors.toMap(data -> (NotificationType) data[0], data -> (String) data[1]));
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
private DatasetRepository datasetRepository;
private BuilderFactory builderFactory;
private UserManager userManager;
private ConfigLoader configLoader;
private Environment environment;
@Autowired
public DatasetManager(ApiContext apiContext, UserManager userManager) {
public DatasetManager(ApiContext apiContext, UserManager userManager, ConfigLoader configLoader, Environment environment) {
this.apiContext = apiContext;
this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
this.datasetRepository = apiContext.getOperationsContext().getDatasetRepository();
this.builderFactory = apiContext.getOperationsContext().getBuilderFactory();
this.userManager = userManager;
this.configLoader = configLoader;
this.environment = environment;
}
public DataTableData<DatasetListingModel> getPaged(DatasetTableRequest datasetTableRequest, Principal principal) throws Exception {
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setLike(datasetTableRequest.getCriteria().getLike());
datasetCriteria.setDatasetTemplates(datasetTableRequest.getCriteria().getDatasetTemplates());
if (datasetTableRequest.getCriteria().getStatus() != null) {
datasetCriteria.setStatus(datasetTableRequest.getCriteria().getStatus().shortValue());
}
datasetCriteria.setDmps(datasetTableRequest.getCriteria().getDmpIds());
datasetCriteria.setGroupIds(datasetTableRequest.getCriteria().getGroupIds());
datasetCriteria.setGrants(datasetTableRequest.getCriteria().getGrants());
datasetCriteria.setCollaborators(datasetTableRequest.getCriteria().getCollaborators());
datasetCriteria.setAllowAllVersions(datasetTableRequest.getCriteria().getAllVersions());
datasetCriteria.setOrganiztions(datasetTableRequest.getCriteria().getOrganisations());
datasetCriteria.setTags(datasetTableRequest.getCriteria().getTags());
if (datasetTableRequest.getCriteria().getIsPublic() != null) {
datasetCriteria.setPublic(datasetTableRequest.getCriteria().getIsPublic());
}
if (datasetTableRequest.getCriteria().getGrantStatus() != null) {
datasetCriteria.setGrantStatus(datasetTableRequest.getCriteria().getGrantStatus());
}
List<eu.eudat.elastic.entities.Dataset> datasets;
try {
datasets = datasetCriteria.getTags() != null && datasetCriteria.getTags().size() > 0 && datasetRepository.exists() ?
datasetRepository.query(datasetCriteria) : new LinkedList<>();
datasets = datasetRepository.exists() ?
datasetRepository.query(datasetCriteria) : null;
} catch (Exception ex) {
logger.warn(ex.getMessage());
datasets = null;
}
UserInfo userInfo = builderFactory.getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
QueryableList<eu.eudat.data.entities.Dataset> items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));
if (datasets != null && datasetTableRequest.getCriteria().getTags() != null && !datasetTableRequest.getCriteria().getTags().isEmpty()) {
// QueryableList<eu.eudat.data.entities.Dataset> items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));
QueryableList<eu.eudat.data.entities.Dataset> items;
if (datasets != null) {
if (!datasets.isEmpty()) {
items = databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class));
List<eu.eudat.elastic.entities.Dataset> finalDatasets = datasets;
items.where((builder, root) -> root.get("id").in(finalDatasets.stream().map(x -> UUID.fromString(x.getId())).collect(Collectors.toList())));
} else
items.where((builder, root) -> root.get("id").in(new UUID[]{UUID.randomUUID()}));
} else {
items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));
//items.where((builder, root) -> root.get("id").in(new UUID[]{UUID.randomUUID()}));
}
} else {
items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));
}
List<Integer> roles = new LinkedList<>();
if (datasetTableRequest.getCriteria().getRole() != null) roles.add(datasetTableRequest.getCriteria().getRole());
QueryableList<eu.eudat.data.entities.Dataset> authItems = databaseRepository.getDatasetDao().getAuthenticated(items, userInfo, roles);
QueryableList<eu.eudat.data.entities.Dataset> pagedItems = PaginationManager.applyPaging(authItems, datasetTableRequest);
DataTableData<DatasetListingModel> dataTable = new DataTableData<DatasetListingModel>();
QueryableList<eu.eudat.data.entities.Dataset> pagedItems;
QueryableList<eu.eudat.data.entities.Dataset> authItems;
if (!datasetTableRequest.getCriteria().getIsPublic()) {
if (principal.getId() == null) {
throw new UnauthorisedException();
}
if (datasetTableRequest.getCriteria().getRole() != null)
roles.add(datasetTableRequest.getCriteria().getRole());
authItems = databaseRepository.getDatasetDao().getAuthenticated(items, userInfo, roles);
pagedItems = PaginationManager.applyPaging(authItems, datasetTableRequest);
} else {
if (principal.getId() != null && datasetTableRequest.getCriteria().getRole() != null) {
items.where((builder, root) -> {
Join userJoin = root.join("dmp", JoinType.LEFT).join("users", JoinType.LEFT);
return builder.and(builder.equal(userJoin.join("user", JoinType.LEFT).get("id"), principal.getId()), builder.equal(userJoin.get("role"), datasetTableRequest.getCriteria().getRole()));
});
}
String[] strings = new String[1];
strings[0] = "-dmp:publishedAt|join|";
datasetTableRequest.getOrderings().setFields(strings);
authItems = items;
pagedItems = PaginationManager.applyPaging(items, datasetTableRequest);
}
DataTableData<DatasetListingModel> dataTable = new DataTableData<>();
CompletableFuture<List<DatasetListingModel>> itemsFuture = pagedItems.
@ -134,23 +198,32 @@ public class DatasetManager {
public DataTableData<DatasetListingModel> getPaged(DatasetPublicTableRequest datasetTableRequest, Principal principal) throws Exception {
DatasetCriteria datasetCriteria = new DatasetCriteria();
datasetCriteria.setTags(datasetTableRequest.getCriteria().getTags());
datasetCriteria.setLike(datasetTableRequest.getCriteria().getLike());
datasetCriteria.setDatasetTemplates(datasetTableRequest.getCriteria().getDatasetProfile());
datasetCriteria.setDmps(datasetTableRequest.getCriteria().getDmpIds());
datasetCriteria.setGrants(datasetTableRequest.getCriteria().getGrants());
List<eu.eudat.elastic.entities.Dataset> datasets;
try {
datasets = datasetCriteria.getTags() != null && datasetCriteria.getTags().size() > 0 && datasetRepository.exists() ?
datasets = datasetRepository.exists() ?
datasetRepository.query(datasetCriteria) : new LinkedList<>();
} catch (Exception ex) {
logger.warn(ex.getMessage());
datasets = null;
}
datasetTableRequest.setQuery(databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class)));
QueryableList<Dataset> items = datasetTableRequest.applyCriteria();
if (datasets != null && datasetTableRequest.getCriteria().getTags() != null && !datasetTableRequest.getCriteria().getTags().isEmpty()) {
/*QueryableList<Dataset> items;
if (datasets != null) {
if (!datasets.isEmpty()) {
items = databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class));
List<eu.eudat.elastic.entities.Dataset> finalDatasets = datasets;
items.where((builder, root) -> root.get("id").in(finalDatasets.stream().map(x -> UUID.fromString(x.getId())).collect(Collectors.toList())));
} else
items = datasetTableRequest.applyCriteria();
items.where((builder, root) -> root.get("id").in(new UUID[]{UUID.randomUUID()}));
}
} else {
items = datasetTableRequest.applyCriteria();
}*/
if (principal.getId() != null && datasetTableRequest.getCriteria().getRole() != null) {
items.where((builder, root) -> {
@ -177,15 +250,20 @@ public class DatasetManager {
return dataTable;
}
public DatasetWizardModel getSingle(String id) {
public DatasetWizardModel getSingle(String id, Principal principal) {
DatasetWizardModel dataset = new DatasetWizardModel();
eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
if (datasetEntity.getDmp().getUsers()
.stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId())
.collect(Collectors.toList()).size() == 0)
throw new UnauthorisedException();
eu.eudat.elastic.entities.Dataset datasetElastic;
try {
datasetElastic = datasetRepository.exists() ?
datasetRepository.findDocument(id) : new eu.eudat.elastic.entities.Dataset();
} catch (Exception ex) {
datasetElastic = new eu.eudat.elastic.entities.Dataset();
logger.warn(ex.getMessage());
datasetElastic = null;
}
dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));
dataset.fromDataModel(datasetEntity);
@ -222,7 +300,13 @@ public class DatasetManager {
boolean latestVersion = profile.getVersion().toString().equals(datasetEntity.getProfile().getVersion().toString());
dataset.setIsProfileLatestVersion(latestVersion);
if (datasetElastic != null && datasetElastic.getTags() != null && !datasetElastic.getTags().isEmpty()) {
dataset.setTags(datasetElastic.getTags());
}
/*if (datasetElastic != null && datasetElastic.getLabel() != null && !datasetElastic.getLabel().isEmpty()) {
dataset.setLabel(datasetElastic.getLabel());
}*/
return dataset;
}
@ -252,11 +336,11 @@ public class DatasetManager {
return pagedDatasetProfile;
}
public File getWordDocument(ConfigLoader configLoader, String id, VisibilityRuleService visibilityRuleService) throws IOException {
private XWPFDocument getWordDocument(ConfigLoader configLoader, eu.eudat.data.entities.Dataset datasetEntity, VisibilityRuleService visibilityRuleService) throws IOException {
WordBuilder wordBuilder = new WordBuilder();
DatasetWizardModel dataset = new DatasetWizardModel();
XWPFDocument document = configLoader.getDocument();
eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
wordBuilder.addParagraphContent(datasetEntity.getLabel(), document, ParagraphStyle.HEADER1, BigInteger.ZERO);
// Space below Dataset title.
@ -327,16 +411,72 @@ public class DatasetManager {
document.removeBodyElement(0);
}
return document;
//FileOutputStream out = new FileOutputStream(exportFile);
// document.write(out);
// out.close();
// return exportFile;
}
private XWPFDocument getLightWordDocument(ConfigLoader configLoader, DatasetWizardModel dataset, VisibilityRuleService visibilityRuleService) throws IOException {
WordBuilder wordBuilder = new WordBuilder();
XWPFDocument document = configLoader.getDocument();
// Space below Dataset title.
XWPFParagraph parBreakDataset = document.createParagraph();
Map<String, Object> properties = new HashMap<>();
if (dataset.getDatasetProfileDefinition() != null) {
JSONObject jObject = new JSONObject(propertiesModelToString(dataset.getDatasetProfileDefinition()));
properties = jObject.toMap();
}
wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
visibilityRuleService.setProperties(properties);
visibilityRuleService.buildVisibilityContext(dataset.getDatasetProfileDefinition().getRules());
wordBuilder.build(document, dataset.getDatasetProfileDefinition(), visibilityRuleService);
// Removes the top empty headings.
for (int i = 0; i < 6; i++) {
document.removeBodyElement(0);
}
return document;
//FileOutputStream out = new FileOutputStream(exportFile);
// document.write(out);
// out.close();
// return exportFile;
}
public File getWordDocumentFile(ConfigLoader configLoader, String id, VisibilityRuleService visibilityRuleService, Principal principal) throws IOException {
eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
if (!datasetEntity.getDmp().isPublic() && datasetEntity.getDmp().getUsers()
.stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId())
.collect(Collectors.toList()).size() == 0)
throw new UnauthorisedException();
String label = datasetEntity.getLabel().replaceAll("[^a-zA-Z0-9+ ]", "");
File exportFile = new File(this.environment.getProperty("temp.temp") + label + ".docx");
XWPFDocument document = getWordDocument(configLoader, datasetEntity, visibilityRuleService);
FileOutputStream out = new FileOutputStream(exportFile);
document.write(out);
out.close();
return exportFile;
}
public FileEnvelope getXmlDocument(String id, VisibilityRuleService visibilityRuleService) throws InstantiationException, IllegalAccessException, IOException {
public String getWordDocumentText (DatasetWizardModel datasetEntity) throws Exception {
XWPFDocument document = getLightWordDocument(this.configLoader, datasetEntity, this.apiContext.getUtilitiesService().getVisibilityRuleService());
XWPFWordExtractor extractor = new XWPFWordExtractor(document);
return extractor.getText();/*.replaceAll("\n\\s*", " ");*/
}
public FileEnvelope getXmlDocument(String id, VisibilityRuleService visibilityRuleService, Principal principal) throws InstantiationException, IllegalAccessException, IOException {
ExportXmlBuilder xmlBuilder = new ExportXmlBuilder();
DatasetWizardModel dataset = new DatasetWizardModel();
eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
if (!datasetEntity.getDmp().isPublic() && datasetEntity.getDmp().getUsers()
.stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId())
.collect(Collectors.toList()).size() == 0)
throw new UnauthorisedException();
Map<String, Object> properties = new HashMap<>();
if (datasetEntity.getProperties() != null) {
JSONObject jobject = new JSONObject(datasetEntity.getProperties());
@ -345,7 +485,7 @@ public class DatasetManager {
PagedDatasetProfile pagedDatasetProfile = getPagedProfile(dataset, datasetEntity);
visibilityRuleService.setProperties(properties);
visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
File file = xmlBuilder.build(pagedDatasetProfile, datasetEntity.getProfile().getId(), visibilityRuleService);
File file = xmlBuilder.build(pagedDatasetProfile, datasetEntity.getProfile().getId(), visibilityRuleService, environment);
FileEnvelope fileEnvelope = new FileEnvelope();
fileEnvelope.setFile(file);
fileEnvelope.setFilename(datasetEntity.getLabel());
@ -400,12 +540,23 @@ public class DatasetManager {
}
public eu.eudat.data.entities.Dataset createOrUpdate(DatasetWizardModel datasetWizardModel, Principal principal) throws Exception {
Boolean sendNotification = false;
Dataset tempDataset = null;
DMP dmp = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(datasetWizardModel.getDmp().getId());
if (datasetWizardModel.getId() != null) {
tempDataset = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().find(datasetWizardModel.getId());
if (tempDataset != null) {
if (datasetWizardModel.getModified().getTime() != tempDataset.getModified().getTime()) {
throw new Exception("Dataset has been modified already by another user.");
}
sendNotification = true;
}
}
if (dmp.getStatus().equals(DMP.DMPStatus.FINALISED.getValue()) && datasetWizardModel.getId() != null)
throw new Exception("DMP is finalized, therefore Dataset cannot be edited.");
eu.eudat.data.entities.Dataset dataset = datasetWizardModel.toDataModel();
dataset.setDmp(dmp);
propertiesModelToString(datasetWizardModel, dataset);
dataset.setProperties(propertiesModelToString(datasetWizardModel.getDatasetProfileDefinition()));
if (datasetWizardModel.getStatus() == (int) Dataset.Status.FINALISED.getValue())
checkDatasetValidation(dataset);
UserInfo userInfo = apiContext.getOperationsContext().getBuilderFactory().getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
@ -415,13 +566,49 @@ public class DatasetManager {
createExternalDatasetsIfTheyDontExist(dataset);
createRegistriesIfTheyDontExist(apiContext.getOperationsContext().getDatabaseRepository().getRegistryDao(), dataset);
createServicesIfTheyDontExist(dataset);
Dataset dataset1 = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().createOrUpdate(dataset);
datasetWizardModel.setId(dataset1.getId());
if (datasetWizardModel.getDmp().getGrant() == null) {
datasetWizardModel.setDmp(new DataManagementPlan().fromDataModelNoDatasets(dataset1.getDmp()));
}
dataset1.setProfile(this.apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(datasetWizardModel.getProfile()));
datasetWizardModel.setDatasetProfileDefinition(getPagedProfile(datasetWizardModel, dataset1));
updateTags(apiContext.getOperationsContext().getDatasetRepository(), datasetWizardModel);
if (sendNotification) {
if (dataset1.getStatus() != Dataset.Status.FINALISED.getValue()) {
this.sendNotification(dataset1, dataset1.getDmp(), userInfo, NotificationType.DATASET_MODIFIED);
} else {
this.sendNotification(dataset1, dataset1.getDmp(), userInfo, NotificationType.DATASET_MODIFIED_FINALISED);
}
}
return dataset1;
}
private void sendNotification(Dataset dataset, DMP dmp, UserInfo user, NotificationType notificationType) {
List<UserDMP> userDMPS = databaseRepository.getUserDmpDao().asQueryable().where(((builder, root) -> builder.equal(root.get("dmp").get("id"), dmp.getId()))).toList();
for (UserDMP userDMP : userDMPS) {
if (!userDMP.getUser().getId().equals(user.getId())) {
Notification notification = new Notification();
notification.setUserId(user);
notification.setType(notificationType);
notification.setNotifyState(NotifyState.PENDING);
notification.setIsActive(ActiveStatus.ACTIVE);
notification.setData("{" +
"\"userId\": \"" + userDMP.getUser().getId() + "\"" +
", \"id\": \"" + dataset.getId() + "\"" +
", \"name\": \"" + dataset.getLabel() + "\"" +
", \"path\": \"" + notificationPaths.get(notificationType) + "\"" +
"}");
notification.setCreatedAt(new Date());
notification.setUpdatedAt(notification.getCreatedAt());
notification.setContactTypeHint(ContactType.EMAIL);
notification.setContactHint(userDMP.getUser().getEmail());
databaseRepository.getNotificationDao().createOrUpdate(notification);
}
}
}
private void checkDatasetValidation(Dataset dataset) throws Exception {
List<String> datasetProfileValidators = new LinkedList<>();
DatasetProfile profile = apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(dataset.getProfile().getId());
@ -446,22 +633,73 @@ public class DatasetManager {
}
}
private void propertiesModelToString(DatasetWizardModel datasetWizardModel, eu.eudat.data.entities.Dataset dataset) {
private String propertiesModelToString(PagedDatasetProfile pagedDatasetProfile) {
Map<String, Object> values = new HashMap();
PagedDatasetProfile properties = datasetWizardModel.getDatasetProfileDefinition();
properties.toMap(values);
pagedDatasetProfile.toMap(values);
JSONObject jobject = new JSONObject(values);
dataset.setProperties(jobject.toString());
return jobject.toString();
}
private void updateTags(DatasetRepository datasetRepository, DatasetWizardModel datasetWizardModel) throws IOException {
if (datasetWizardModel.getTags() != null && !datasetWizardModel.getTags().isEmpty()) {
public void updateTags(DatasetRepository datasetRepository, DatasetWizardModel datasetWizardModel) throws Exception {
// if (datasetWizardModel.getTags() != null && !datasetWizardModel.getTags().isEmpty()) {
eu.eudat.elastic.entities.Dataset dataset = new eu.eudat.elastic.entities.Dataset();
dataset.setId(datasetWizardModel.getId().toString());
if (datasetWizardModel.getTags() != null && !datasetWizardModel.getTags().isEmpty()) {
DatasetCriteria criteria = new DatasetCriteria();
criteria.setTags(datasetWizardModel.getTags());
List<Tag> tags = apiContext.getOperationsContext().getDatasetRepository().query(criteria).stream().map(eu.eudat.elastic.entities.Dataset::getTags).flatMap(Collection::stream)
.filter(StreamDistinctBy.distinctByKey(Tag::getId)).filter(tag -> datasetWizardModel.getTags().stream().anyMatch(tag1 -> tag1.getName().equals(tag.getName()))).collect(Collectors.toList());
if (tags.isEmpty()) {
datasetWizardModel.getTags().forEach(tag -> tag.setId(UUID.randomUUID().toString()));
dataset.setTags(datasetWizardModel.getTags());
} else {
dataset.setTags(tags);
}
}
dataset.setLabel(datasetWizardModel.getLabel());
dataset.setDescription(datasetWizardModel.getDescription());
dataset.setTemplate(datasetWizardModel.getProfile());
dataset.setStatus(datasetWizardModel.getStatus());
dataset.setDmp(datasetWizardModel.getDmp().getId());
dataset.setGroup(datasetWizardModel.getDmp().getGroupId());
dataset.setGrant(datasetWizardModel.getDmp().getGrant().getId());
if (datasetWizardModel.getDmp().getUsers() != null) {
dataset.setCollaborators(datasetWizardModel.getDmp().getUsers().stream().map(user -> {
Collaborator collaborator = new Collaborator();
collaborator.setId(user.getId().toString());
collaborator.setName(user.getName());
return collaborator;
}).collect(Collectors.toList()));
}
DataManagementPlanCriteria dmpCriteria = new DataManagementPlanCriteria();
dmpCriteria.setAllVersions(true);
dmpCriteria.setGroupIds(Collections.singletonList(datasetWizardModel.getDmp().getGroupId()));
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(dmpCriteria).toList().stream()
.max(Comparator.comparing(DMP::getVersion)).ifPresent(dmp -> dataset.setLastVersion(dmp.getId().equals(datasetWizardModel.getDmp().getId())));
apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(dmpCriteria).toList().stream().filter(DMP::isPublic)
.max(Comparator.comparing(DMP::getVersion)).ifPresent(dmp -> dataset.setLastPublicVersion(dmp.getId().equals(datasetWizardModel.getDmp().getId())));
if (dataset.getLastVersion() == null) {
dataset.setLastVersion(true);
}
if (dataset.getLastPublicVersion() == null) {
dataset.setLastPublicVersion(false);
}
if (datasetWizardModel.getDmp().getOrganisations() != null) {
dataset.setOrganizations(datasetWizardModel.getDmp().getOrganisations().stream().map(org -> {
Organization organization = new Organization();
organization.setId(org.getId());
organization.setName(org.getName());
return organization;
}).collect(Collectors.toList()));
}
dataset.setPublic(datasetWizardModel.getDmp().getPublic());
dataset.setGrantStatus(datasetWizardModel.getDmp().getGrant().getStatus());
dataset.setFormData(this.getWordDocumentText(datasetWizardModel));
datasetRepository.createOrUpdate(dataset);
// }
}
}
private void createRegistriesIfTheyDontExist(RegistryDao registryDao, eu.eudat.data.entities.Dataset dataset) {
if (dataset.getRegistries() != null && !dataset.getRegistries().isEmpty()) {
@ -544,8 +782,8 @@ public class DatasetManager {
datasetDao.createOrUpdate(dataset);
}
public ResponseEntity<byte[]> getDocument(String id, VisibilityRuleService visibilityRuleService, String contentType) throws IllegalAccessException, IOException, InstantiationException {
FileEnvelope envelope = getXmlDocument(id, visibilityRuleService);
public ResponseEntity<byte[]> getDocument(String id, VisibilityRuleService visibilityRuleService, String contentType, Principal principal) throws IllegalAccessException, IOException, InstantiationException {
FileEnvelope envelope = getXmlDocument(id, visibilityRuleService, principal);
InputStream resource = new FileInputStream(envelope.getFile());
logger.info("Mime Type of " + envelope.getFilename() + " is " +
new MimetypesFileTypeMap().getContentType(envelope.getFile()));
@ -645,7 +883,8 @@ public class DatasetManager {
datasetElastic = datasetRepository.exists() ?
datasetRepository.findDocument(id) : new eu.eudat.elastic.entities.Dataset();
} catch (Exception ex) {
datasetElastic = new eu.eudat.elastic.entities.Dataset();
logger.warn(ex.getMessage());
datasetElastic = null;
}
dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));
dataset.fromDataModel(datasetEntity);
@ -667,7 +906,12 @@ public class DatasetManager {
// Now at latest version.
dataset.setIsProfileLatestVersion(true);
if (datasetElastic != null && datasetElastic.getTags() != null && !datasetElastic.getTags().isEmpty()) {
dataset.setTags(datasetElastic.getTags());
}
/*if (datasetElastic != null && datasetElastic.getLabel() != null && !datasetElastic.getLabel().isEmpty()) {
dataset.setLabel(datasetElastic.getLabel());
}*/
return dataset;
}
@ -697,4 +941,37 @@ public class DatasetManager {
return data;
}
public void generateIndex(Principal principal) {
if (principal.getAuthorities().contains(Authorities.ADMIN.getValue())) {
this.apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().asQueryable().toList();
List<DatasetWizardModel> datasetWizardModels = this.apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().asQueryable().toList()
.stream().map(dataset -> {
DatasetWizardModel datasetWizardModel = new DatasetWizardModel().fromDataModel(dataset);
datasetWizardModel.setDatasetProfileDefinition(getPagedProfile(datasetWizardModel, dataset));
return datasetWizardModel;
}).collect(Collectors.toList());
datasetWizardModels.forEach(datasetWizardModel -> {
try {
eu.eudat.elastic.entities.Dataset dataset = apiContext.getOperationsContext().getDatasetRepository().findDocument(datasetWizardModel.getId().toString());
if (dataset != null) {
datasetWizardModel.setTags(dataset.getTags());
}
updateTags(apiContext.getOperationsContext().getDatasetRepository(), datasetWizardModel);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
});
}
}
public void clearIndex(Principal principal) {
if (principal.getAuthorities().contains(Authorities.ADMIN.getValue())) {
try {
this.apiContext.getOperationsContext().getDatasetRepository().clear();
} catch (IOException e) {
logger.error(e.getMessage(), e);
}
}
}
}

4
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetProfileManager.java
View File

@ -113,8 +113,8 @@ public class DatasetProfileManager {
ResponseEntity<Object> response = restTemplate.exchange(data.getUrl() + "?search=" + like, HttpMethod.GET, entity, Object.class);
DocumentContext jsonContext = JsonPath.parse(response.getBody());
List<Map<String, String>> jsonItems = jsonContext.read(data.getOptionsRoot() + "['" + data.getAutoCompleteOptions().getLabel() + "','" + data.getAutoCompleteOptions().getValue() + "','" + data.getAutoCompleteOptions().getSource() + "']");
jsonItems.forEach(item -> result.add(new ExternalAutocompleteFieldModel(item.get(data.getAutoCompleteOptions().getValue()), item.get(data.getAutoCompleteOptions().getLabel()), item.get(data.getAutoCompleteOptions().getSource()))));
List<Map<String, String>> jsonItems = jsonContext.read(data.getOptionsRoot() + "['" + data.getAutoCompleteOptions().getLabel() + "','" + data.getAutoCompleteOptions().getValue() + "','" + data.getAutoCompleteOptions().getSource() + "','" + "uri" + "']");
jsonItems.forEach(item -> result.add(new ExternalAutocompleteFieldModel(item.get(data.getAutoCompleteOptions().getValue()), item.get(data.getAutoCompleteOptions().getLabel()), item.get(data.getAutoCompleteOptions().getSource()), item.get("uri"))));
return result;
}

10
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetWizardManager.java
View File

@ -15,6 +15,7 @@ import eu.eudat.models.data.dmp.DataManagementPlan;
import eu.eudat.models.data.security.Principal;
import eu.eudat.queryable.QueryableList;
import java.io.IOException;
import java.util.LinkedList;
import java.util.List;
import java.util.UUID;
@ -47,9 +48,14 @@ public class DatasetWizardManager {
return;
}
public void delete(ApiContext apiContext, UUID uuid) {
public void delete(ApiContext apiContext, UUID uuid) throws IOException {
Dataset oldDataset = apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().find(uuid);
oldDataset.setStatus(DMP.DMPStatus.DELETED.getValue());
eu.eudat.elastic.entities.Dataset oldDatasetElasitc = apiContext.getOperationsContext().getDatasetRepository().findDocument(uuid.toString());
oldDataset.setStatus(Dataset.Status.DELETED.getValue());
oldDatasetElasitc.setStatus(oldDataset.getStatus());
apiContext.getOperationsContext().getDatabaseRepository().getDatasetDao().createOrUpdate(oldDataset);
if (uuid != null && oldDatasetElasitc.getId()!= null) {
apiContext.getOperationsContext().getDatasetRepository().createOrUpdate(oldDatasetElasitc);
}
}
}

6
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DocumentManager.java
View File

@ -43,11 +43,13 @@ public class DocumentManager {
private ApiContext context;
private DatasetManager datasetManager;
private ConfigLoader configLoader;
private Environment environment;
public DocumentManager(ApiContext context, DatasetManager datasetManager, ConfigLoader configLoader) {
public DocumentManager(ApiContext context, DatasetManager datasetManager, ConfigLoader configLoader, Environment environment) {
this.context = context;
this.datasetManager = datasetManager;
this.configLoader = configLoader;
this.environment = environment;
}
public File getWordDocument(ConfigLoader configLoader, DatasetDao datatasetRepository, String id, VisibilityRuleService visibilityRuleService) throws InstantiationException, IllegalAccessException, IOException {
@ -82,7 +84,7 @@ public class DocumentManager {
PagedDatasetProfile pagedDatasetProfile = datasetManager.getPagedProfile(dataset, datasetEntity);
visibilityRuleService.setProperties(properties);
visibilityRuleService.buildVisibilityContext(pagedDatasetProfile.getRules());
File file = xmlBuilder.build(pagedDatasetProfile, UUID.fromString(id), visibilityRuleService);
File file = xmlBuilder.build(pagedDatasetProfile, UUID.fromString(id), visibilityRuleService, environment);
FileEnvelope fileEnvelope = new FileEnvelope();
fileEnvelope.setFile(file);
fileEnvelope.setFilename(datasetEntity.getLabel());

123
dmp-backend/web/src/main/java/eu/eudat/logic/managers/LockManager.java Normal file
View File

@ -0,0 +1,123 @@
package eu.eudat.logic.managers;
import eu.eudat.data.dao.criteria.LockCriteria;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.lock.Lock;
import eu.eudat.models.data.security.Principal;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Component;
import javax.persistence.NoResultException;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@Component
public class LockManager {
private final Comparator<eu.eudat.data.entities.Lock> compareByTouchedAt = Comparator.comparing(o -> o.getTouchedAt().getTime());
private ApiContext apiContext;
private Environment environment;
@Autowired
public LockManager(ApiContext apiContext, Environment environment) {
this.apiContext = apiContext;
this.environment = environment;
}
public eu.eudat.data.entities.Lock createOrUpdate(Lock lock, Principal principal) throws Exception {
if (lock.getId() != null) {
try {
eu.eudat.data.entities.Lock entity = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().find(lock.getId());
if (entity != null) {
if (!entity.getLockedBy().getId().equals(principal.getId())) {
throw new Exception("Is not locked by that user");
}
}
}catch(NoResultException e) {
lock.setId(null);
}
}
eu.eudat.data.entities.Lock newLock = lock.toDataModel();
newLock = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().createOrUpdate(newLock);
return newLock;
}
public boolean isLocked(String targetId, Principal principal) throws Exception {
LockCriteria criteria = new LockCriteria();
criteria.setTarget(UUID.fromString(targetId));
Long availableLocks = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).count();
if (availableLocks == 1) {
eu.eudat.data.entities.Lock lock = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).getSingle();
if (lock.getLockedBy().getId().equals(principal.getId())) {
lock.setTouchedAt(new Date());
this.createOrUpdate(new Lock().fromDataModel(lock), principal);
return false;
}
return this.forceUnlock(targetId) > 0;
} else if (availableLocks > 1) {
this.forceUnlock(targetId);
return this.isLocked(targetId, principal);
}
return false;
}
private Long forceUnlock(String targetId) {
LockCriteria criteria = new LockCriteria();
criteria.setTarget(UUID.fromString(targetId));
Long availableLocks = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).count();
long deletedLocks = 0L;
if (availableLocks > 0) {
List<eu.eudat.data.entities.Lock> locks = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).toList();
for (eu.eudat.data.entities.Lock lock : locks) {
if (new Date().getTime() - lock.getTouchedAt().getTime() > environment.getProperty("database.lock-fail-interval", Integer.class)) {
this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().delete(lock);
deletedLocks++;
}
}
if (deletedLocks == 0) {
eu.eudat.data.entities.Lock recentlock = locks.stream().max(compareByTouchedAt).get();
for (eu.eudat.data.entities.Lock lock : locks) {
if (lock != recentlock) {
this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().delete(lock);
deletedLocks++;
}
}
}
}
return availableLocks - deletedLocks;
}
public void unlock(String targetId, Principal principal) throws Exception {
LockCriteria criteria = new LockCriteria();
criteria.setTarget(UUID.fromString(targetId));
Long availableLocks = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).count();
if (availableLocks == 1) {
eu.eudat.data.entities.Lock lock = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).getSingle();
if (!lock.getLockedBy().getId().equals(principal.getId())) {
throw new Exception("Only the user who created that lock can delete it");
}
this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().delete(lock);
} else if (availableLocks > 1) {
List<eu.eudat.data.entities.Lock> locks = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).toList();
locks.stream().filter(lock -> lock.getLockedBy().getId().equals(principal.getId())).forEach(lock -> this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().delete(lock));
}
}
public Lock getFromTarget(String targetId, Principal principal) throws Exception {
LockCriteria criteria = new LockCriteria();
criteria.setTarget(UUID.fromString(targetId));
Long availableLocks = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).count();
if (availableLocks > 0) {
eu.eudat.data.entities.Lock lock = this.apiContext.getOperationsContext().getDatabaseRepository().getLockDao().getWithCriteria(criteria).getSingle();
if (!lock.getLockedBy().getId().equals(principal.getId())) {
throw new Exception("Only the user who created that lock can access it");
}
return new Lock().fromDataModel(lock);
}
return null;
}
}

124
dmp-backend/web/src/main/java/eu/eudat/logic/managers/NotificationManager.java Normal file
View File

@ -0,0 +1,124 @@
package eu.eudat.logic.managers;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.entities.Notification;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.data.enumeration.notification.ActiveStatus;
import eu.eudat.data.enumeration.notification.NotifyState;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.utilities.MailService;
import eu.eudat.models.data.mail.SimpleMail;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Component;
import javax.mail.MessagingException;
import javax.transaction.Transactional;
import java.io.IOException;
import java.util.*;
@Component
public class NotificationManager {
private static final Logger logger = LoggerFactory.getLogger(NotificationManager.class);
private ApiContext apiContext;
private Environment environment;
private MailService mailService;
@Autowired
public NotificationManager(ApiContext apiContext, Environment environment, MailService mailService) {
this.apiContext = apiContext;
this.environment = environment;
this.mailService = mailService;
}
@Transactional
public void sendNotification(Notification notification) throws Exception {
if (notification.getNotifyState() == NotifyState.ERROR) {
if (notification.getRetryCount() == null) {
notification.setRetryCount(0);
}
notification.setRetryCount(notification.getRetryCount() + 1);
if (notification.getRetryCount() >= this.environment.getProperty("notification.maxRetries", Integer.class)) {
notification.setIsActive(ActiveStatus.INACTIVE);
notification.setUpdatedAt(new Date());
return;
}
}
notification.setNotifyState(NotifyState.PROCESSING);
notification.setNotifiedAt(new Date());
notification.setUpdatedAt(new Date());
try {
Map<String, String> data = new ObjectMapper().readValue(notification.getData(), HashMap.class);
UserInfo userInfo = this.apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(UUID.fromString(data.get("userId")));
String subjectTemplate = "";
String contentTemplate = "";
switch (notification.getType()) {
case DMP_MODIFIED:
case DATASET_MODIFIED:
subjectTemplate = this.environment.getProperty("notification.modified.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/modifiedNotification.html");
break;
case DMP_PUBLISH:
subjectTemplate = this.environment.getProperty("notification.publish.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/publishNotification.html");
break;
case DMP_FINALISED:
subjectTemplate = this.environment.getProperty("notification.finalised.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/finalisedNotification.html");
break;
case DMP_MODIFIED_FINALISED:
case DATASET_MODIFIED_FINALISED:
subjectTemplate = this.environment.getProperty("notification.modifiedFinalised.subject");
contentTemplate = mailService.getMailTemplateContent("classpath:templates/notifications/modifiedFinalisedNotification.html");
break;
}
switch (notification.getContactTypeHint()) {
case EMAIL:
this.sendEmailNotification(notification, userInfo, data, subjectTemplate, contentTemplate);
break;
}
}catch (Exception e) {
notification.setNotifyState(NotifyState.ERROR);
notification.setUpdatedAt(new Date());
logger.error(e.getMessage(), e);
}
}
private void sendEmailNotification(Notification notification, UserInfo userInfo, Map<String, String> data, String subjectTemplate, String contentTemplate) throws IOException {
SimpleMail simpleMail = new SimpleMail();
simpleMail.setFrom(this.environment.getProperty("mail.from"));
simpleMail.setSubject(makeSubject(data, subjectTemplate));
simpleMail.setTo(notification.getContactHint());
simpleMail.setContent(makeContent(data, notification, userInfo, contentTemplate));
try {
mailService.sendSimpleMail(simpleMail);
notification.setNotifyState(NotifyState.SUCCEEDED);
notification.setUpdatedAt(new Date());
} catch (MessagingException e) {
notification.setNotifyState(NotifyState.ERROR);
notification.setUpdatedAt(new Date());
logger.error(e.getMessage(), e);
}
}
private String makeSubject(Map<String, String> data, String subjectTemplate) {
return subjectTemplate.replace("{name}", data.get("name"));
}
private String makeContent(Map<String, String> data, Notification notification, UserInfo userInfo, String template) {
String content = template;
content = content.replace("{recipient}", userInfo.getName());
for (String key : data.keySet()) {
content = content.replace("{" + key +"}", data.get(key));
}
content = content.replace("{host}", this.environment.getProperty("dmp.domain"));
content = content.replace("{reasonName}", notification.getUserId().getName());
return content;
}
}

47
dmp-backend/web/src/main/java/eu/eudat/logic/managers/RDAManager.java Normal file
View File

@ -0,0 +1,47 @@
package eu.eudat.logic.managers;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.entities.DMP;
import eu.eudat.models.rda.Dmp;
import eu.eudat.models.rda.RDAModel;
import eu.eudat.models.rda.mapper.DmpRDAMapper;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import javax.transaction.Transactional;
import java.io.IOException;
import java.text.SimpleDateFormat;
@Component
public class RDAManager {
private DmpRDAMapper dmpRDAMapper;
@Autowired
public RDAManager(DmpRDAMapper dmpRDAMapper) {
this.dmpRDAMapper = dmpRDAMapper;
}
@Transactional
public String convertToRDA(DMP dmp) throws JsonProcessingException {
String result = "";
Dmp rdaDmp = dmpRDAMapper.toRDA(dmp);
ObjectMapper mapper = new ObjectMapper();
mapper.setDateFormat(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss Z"));
result = mapper.writeValueAsString(rdaDmp);
return result;
}
public DMP convertToEntity(String json) throws IOException {
ObjectMapper mapper = new ObjectMapper();
mapper.setDateFormat(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss Z"));
Dmp rda = mapper.readValue(json, Dmp.class);
return dmpRDAMapper.toEntity(rda);
}
}

6
dmp-backend/web/src/main/java/eu/eudat/logic/managers/UserManager.java
View File

@ -1,6 +1,7 @@
package eu.eudat.logic.managers;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.data.dao.criteria.DataManagementPlanCriteria;
import eu.eudat.data.dao.entities.UserInfoDao;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.UserInfo;
@ -64,7 +65,10 @@ public class UserManager {
eu.eudat.data.entities.UserInfo user = apiContext.getOperationsContext().getDatabaseRepository().getUserInfoDao().find(userId);
UserProfile profile = new UserProfile().fromDataModel(user);
List<Integer> roles = new LinkedList<>();
List<DMP> dmps = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().asQueryable(), userId, roles).take(5).toList();
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
criteria.setAllVersions(false);
QueryableList<DMP> items = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getWithCriteria(criteria);
List<DMP> dmps = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().getAuthenticated(items, userId, roles).take(5).toList();
profile.setAssociatedDmps(dmps.stream().map(x -> new DataManagementPlan().fromDataModel(x)).collect(Collectors.toList()));
return profile;
}

27
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/DataFieldsUrlConfiguration.java
View File

@ -12,6 +12,9 @@ public class DataFieldsUrlConfiguration {
private String description;
private String source;
private String count;
private String path;
private String host;
private String types;
public String getId() {
return id;
@ -67,4 +70,28 @@ public class DataFieldsUrlConfiguration {
public void setCount(String count) {
this.count = count;
}
public String getPath() {
return path;
}
@XmlElement(name = "path")
public void setPath(String path) {
this.path = path;
}
public String getHost() {
return host;
}
@XmlElement(name = "host")
public void setHost(String host) {
this.host = host;
}
@XmlElement(name = "types")
public String getTypes() {
return types;
}
public void setTypes(String types) {
this.types = types;
}
}

53
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/DataUrlConfiguration.java
View File

@ -1,6 +1,8 @@
package eu.eudat.logic.proxy.config;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import java.util.List;
/**
* Created by ikalyvas on 6/29/2018.
@ -8,6 +10,11 @@ import javax.xml.bind.annotation.XmlElement;
public class DataUrlConfiguration {
private String path;
private DataFieldsUrlConfiguration fieldsUrlConfiguration;
private UrlConfiguration urlConfiguration;
private String parseClass;
private String parseField;
private List<String> mergedFields;
private String mergedFieldName;
public String getPath() {
return path;
@ -26,4 +33,50 @@ public class DataUrlConfiguration {
public void setFieldsUrlConfiguration(DataFieldsUrlConfiguration fieldsUrlConfiguration) {
this.fieldsUrlConfiguration = fieldsUrlConfiguration;
}
public UrlConfiguration getUrlConfiguration() {
return urlConfiguration;
}
@XmlElement(name = "urlConfig")
public void setUrlConfiguration(UrlConfiguration urlConfiguration) {
this.urlConfiguration = urlConfiguration;
}
public String getParseClass() {
return parseClass;
}
@XmlElement(name = "parse-class")
public void setParseClass(String parseClass) {
this.parseClass = parseClass;
}
public String getParseField() {
return parseField;
}
@XmlElement(name = "parse-field")
public void setParseField(String parseField) {
this.parseField = parseField;
}
public List<String> getMergedFields() {
return mergedFields;
}
@XmlElementWrapper(name = "merge-fields")
@XmlElement(name = "field")
public void setMergedFields(List<String> mergedFields) {
this.mergedFields = mergedFields;
}
public String getMergedFieldName() {
return mergedFieldName;
}
@XmlElement(name = "merge-field-name")
public void setMergedFieldName(String mergedFieldName) {
this.mergedFieldName = mergedFieldName;
}
}

18
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/ExternalUrlCriteria.java
View File

@ -5,6 +5,8 @@ public class ExternalUrlCriteria {
private String page;
private String pageSize;
private String funderId;
private String path;
private String host;
public String getLike() {
return like;
@ -34,6 +36,22 @@ public class ExternalUrlCriteria {
this.funderId = funderId;
}
public String getPath() {
return path;
}
public void setPath(String path) {
this.path = path;
}
public String getHost() {
return host;
}
public void setHost(String host) {
this.host = host;
}
public ExternalUrlCriteria(String like) {
this.like = like;
}

129
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/fetching/RemoteFetcher.java
View File

@ -4,19 +4,25 @@ import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import eu.eudat.logic.proxy.config.*;
import eu.eudat.logic.proxy.config.DataUrlConfiguration;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.FetchStrategy;
import eu.eudat.logic.proxy.config.UrlConfiguration;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import net.minidev.json.JSONArray;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.stereotype.Service;
import java.io.File;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
import java.beans.PropertyDescriptor;
import java.io.*;
import java.lang.reflect.Method;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
@ -154,10 +160,11 @@ public class RemoteFetcher {
private String replaceCriteriaOnUrl(String path, ExternalUrlCriteria externalUrlCriteria, String firstPage) {
String completedPath = path;
if (externalUrlCriteria.getLike() != null) {
if (path.contains("openaire") && externalUrlCriteria.getLike().equals(""))
if ((path.contains("openaire") || path.contains("orcid") || path.contains("ror")) && externalUrlCriteria.getLike().equals("")) {
completedPath = completedPath.replaceAll("\\{like}", "*");
else
} else {
completedPath = completedPath.replaceAll("\\{like}", externalUrlCriteria.getLike());
}
} else {
completedPath = completedPath.replace("{like}", "");
}
@ -184,6 +191,16 @@ public class RemoteFetcher {
} else {
completedPath = completedPath.replace("{pageSize}", "60");
}
if (externalUrlCriteria.getHost() != null) {
completedPath = completedPath.replace("{host}", externalUrlCriteria.getHost());
} else {
completedPath = completedPath.replace("{host}", "");
}
if (externalUrlCriteria.getPath() != null) {
completedPath = completedPath.replace("{path}", externalUrlCriteria.getPath());
} else {
completedPath = completedPath.replace("{path}", "");
}
return completedPath;
}
@ -225,13 +242,17 @@ public class RemoteFetcher {
HttpURLConnection con = (HttpURLConnection) url.openConnection();
con.setRequestMethod("GET");
if (contentType != null && !contentType.isEmpty()) {
con.setRequestProperty("Accept", contentType);
}
int responseCode = con.getResponseCode();
if (responseCode == HttpURLConnection.HTTP_OK) { // success
//do here all the parsing
Results results = new Results();
if (con.getHeaderField("Content-Type").contains("json")) {
DocumentContext jsonContext = JsonPath.parse(con.getInputStream());
Results results;
if (jsonDataPath.getFieldsUrlConfiguration().getSource() != null) {
results = new Results(jsonContext.read(jsonDataPath.getPath()
+ "[" + jsonDataPath.getFieldsUrlConfiguration().getName() + "," + jsonDataPath.getFieldsUrlConfiguration().getDescription()
@ -243,6 +264,42 @@ public class RemoteFetcher {
+ "[" + jsonDataPath.getFieldsUrlConfiguration().getName()
+ "," + jsonDataPath.getFieldsUrlConfiguration().getId() + "]"),
new HashMap<>(1, 1));
} else if (jsonDataPath.getFieldsUrlConfiguration().getPath() != null) {
results = new Results(jsonContext.read(jsonDataPath.getPath()
+ "[" + jsonDataPath.getFieldsUrlConfiguration().getPath()
+ "," + jsonDataPath.getFieldsUrlConfiguration().getHost() + "]"),
new HashMap<>(1, 1));
List<Map<String, String>> multiResults = results.results.stream().map(result -> {
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria();
externalUrlCriteria.setPath(result.get("path"));
externalUrlCriteria.setHost(result.get("host"));
String replacedPath = replaceCriteriaOnUrl(jsonDataPath.getUrlConfiguration().getUrl(), externalUrlCriteria, jsonDataPath.getUrlConfiguration().getFirstpage());
return getResultsFromUrl(replacedPath, jsonDataPath.getUrlConfiguration().getData(), jsonDataPath.getUrlConfiguration().getData().getPath(), jsonDataPath.getUrlConfiguration().getContentType());
}).filter(Objects::nonNull).map(results1 -> results1.results.get(0)).collect(Collectors.toList());
results = new Results(multiResults, new HashMap<>(1, 1));
} else if (jsonDataPath.getFieldsUrlConfiguration().getTypes() != null) {
List<Map<String, Object>> tempRes = jsonContext.read(jsonDataPath.getPath()
+ "[" + jsonDataPath.getFieldsUrlConfiguration().getId() + "," + jsonDataPath.getFieldsUrlConfiguration().getName()
+ "," + jsonDataPath.getFieldsUrlConfiguration().getTypes() + "," + jsonDataPath.getFieldsUrlConfiguration().getUri() + "]");
List<Map<String, String>> finalRes = new ArrayList<>();
tempRes.forEach(map -> {
Map<String, String> resMap = new HashMap<>();
map.forEach((key, value) -> {
if (key.equals(jsonDataPath.getFieldsUrlConfiguration().getTypes().substring(1, jsonDataPath.getFieldsUrlConfiguration().getTypes().length() - 1))) {
resMap.put("tags", ((JSONArray) value).toJSONString());
} else if (key.equals(jsonDataPath.getFieldsUrlConfiguration().getUri().substring(1, jsonDataPath.getFieldsUrlConfiguration().getTypes().length() - 1))) {
resMap.put(key, ((JSONArray) value).toJSONString());
} else {
resMap.put(key, (String) value);
}
});
finalRes.add(resMap);
});
results = new Results(finalRes,
new HashMap<>(1, 1));
} else {
results = new Results(jsonContext.read(jsonDataPath.getPath()
+ "[" + jsonDataPath.getFieldsUrlConfiguration().getName() + "," + jsonDataPath.getFieldsUrlConfiguration().getDescription()
@ -251,6 +308,58 @@ public class RemoteFetcher {
}
results.results = results.results.stream().map(e -> e.entrySet().stream().collect(Collectors.toMap(x -> this.transformKey(jsonDataPath,x.getKey()), Map.Entry::getValue)))
.collect(Collectors.toList());
} else if (con.getHeaderField("Content-Type").contains("xml")) {
Class<?> aClass = Class.forName(jsonDataPath.getParseClass());
JAXBContext jaxbContext = JAXBContext.newInstance(aClass);
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
Object data = unmarshaller.unmarshal(con.getInputStream());
Method reader = null;
if (jsonDataPath.getParseField() != null && !jsonDataPath.getParseField().isEmpty()) {
reader = new PropertyDescriptor(jsonDataPath.getParseField(), aClass).getReadMethod();
}
ObjectMapper objectMapper = new ObjectMapper();
List<Map<String, String>> values = new ArrayList<>();
int max = 1;
if (reader != null) {
Object invokedField = reader.invoke(data);
if (invokedField instanceof Collection) {
max = ((Collection) invokedField).size();
}
}
for (int i = 0; i< max; i++) {
Object value;
if (reader != null) {
Object invokedField = reader.invoke(data);
if (invokedField instanceof Collection) {
value = ((Collection) invokedField).toArray()[i];
} else {
value = invokedField;
}
} else {
value = data;
}
Map<String, String> map = objectMapper.convertValue(value, Map.class);
if (jsonDataPath.getMergedFields() != null && !jsonDataPath.getMergedFields().isEmpty() && jsonDataPath.getMergedFieldName() != null && !jsonDataPath.getMergedFieldName().isEmpty()) {
Map<String, String> finalMap = new HashMap<>();
for (Map.Entry<String, String> entry : map.entrySet()) {
if (jsonDataPath.getMergedFields().contains(entry.getKey())) {
if (!finalMap.containsKey(jsonDataPath.getMergedFieldName())) {
finalMap.put(jsonDataPath.getMergedFieldName(), entry.getValue());
} else {
finalMap.put(jsonDataPath.getMergedFieldName(), finalMap.get(jsonDataPath.getMergedFieldName()) + " " + entry.getValue());
}
} else {
finalMap.put(entry.getKey(), entry.getValue());
}
}
values.add(finalMap);
} else {
values.add(map);
}
}
results = new Results(values, new HashMap<>(1, 1));
}
return results;
}
} catch (MalformedURLException e1) {
@ -302,6 +411,8 @@ public class RemoteFetcher {
if (dataUrlConfiguration.getFieldsUrlConfiguration().getName() != null && key.equals(dataUrlConfiguration.getFieldsUrlConfiguration().getName().replace("'",""))) return "name";
if (dataUrlConfiguration.getFieldsUrlConfiguration().getSource() != null && key.equals(dataUrlConfiguration.getFieldsUrlConfiguration().getSource().replace("'",""))) return "source";
if (dataUrlConfiguration.getFieldsUrlConfiguration().getCount() != null && key.equals(dataUrlConfiguration.getFieldsUrlConfiguration().getCount().replace("'",""))) return "count";
if (dataUrlConfiguration.getFieldsUrlConfiguration().getPath() != null && key.equals(dataUrlConfiguration.getFieldsUrlConfiguration().getPath().replace("'",""))) return "path";
if (dataUrlConfiguration.getFieldsUrlConfiguration().getHost() != null && key.equals(dataUrlConfiguration.getFieldsUrlConfiguration().getHost().replace("'",""))) return "host";
return null;
}
@ -311,8 +422,8 @@ public class RemoteFetcher {
Map<String, Integer> pagination;
Results() {
this.results = new ArrayList<Map<String, String>>();
this.pagination = new HashMap<String, Integer>();
this.results = new ArrayList<>();
this.pagination = new HashMap<>();
}
Results(List<Map<String, String>> results, Map<String, Integer> pagination) {

4
dmp-backend/web/src/main/java/eu/eudat/logic/services/operations/DatabaseRepository.java
View File

@ -52,5 +52,9 @@ public interface DatabaseRepository {
FunderDao getFunderDao();
LockDao getLockDao();
NotificationDao getNotificationDao();
<T> void detachEntity(T entity);
}

22
dmp-backend/web/src/main/java/eu/eudat/logic/services/operations/DatabaseRepositoryImpl.java
View File

@ -35,6 +35,8 @@ public class DatabaseRepositoryImpl implements DatabaseRepository {
private LoginConfirmationEmailDao loginConfirmationEmailDao;
private ProjectDao projectDao;
private FunderDao funderDao;
private LockDao lockDao;
private NotificationDao notificationDao;
private EntityManager entityManager;
@ -273,6 +275,26 @@ public class DatabaseRepositoryImpl implements DatabaseRepository {
this.funderDao = funderDao;
}
@Autowired
public void setLockDao(LockDao lockDao) {
this.lockDao = lockDao;
}
@Override
public LockDao getLockDao() {
return lockDao;
}
@Override
public NotificationDao getNotificationDao() {
return notificationDao;
}
@Autowired
public void setNotificationDao(NotificationDao notificationDao) {
this.notificationDao = notificationDao;
}
public <T> void detachEntity(T entity) {
this.entityManager.detach(entity);
}

2
dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/ConfirmationEmailServiceImpl.java
View File

@ -56,7 +56,7 @@ public class ConfirmationEmailServiceImpl implements ConfirmationEmailService {
}
private String createContent(UUID confirmationToken, MailService mailService) {
String content = mailService.getMailTemplateContent("classpath:emailConfirmation.html");
String content = mailService.getMailTemplateContent("classpath:templates/email/emailConfirmation.html");
content = content.replace("{confirmationToken}", confirmationToken.toString());
content = content.replace("{expiration_time}", secondsToTime(Integer.parseInt(this.environment.getProperty("conf_email.expiration_time_seconds"))));
content = content.replace("{host}", this.environment.getProperty("dmp.domain"));

2
dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/InvitationServiceImpl.java
View File

@ -71,7 +71,7 @@ public class InvitationServiceImpl implements InvitationService {
return CompletableFuture.runAsync(() -> {
SimpleMail mail = new SimpleMail();
mail.setSubject(createSubject(dmp, mailService.getMailTemplateSubject()));
mail.setContent(createContent(invitation.getId(), dmp, recipient, mailService.getMailTemplateContent("classpath:email.html")));
mail.setContent(createContent(invitation.getId(), dmp, recipient, mailService.getMailTemplateContent("classpath:templates/email/email.html")));
mail.setTo(invitation.getInvitationEmail());
try {
mailService.sendSimpleMail(mail);

3
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/builders/XmlBuilder.java
View File

@ -12,6 +12,7 @@ import org.xml.sax.SAXException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
@ -47,6 +48,8 @@ public class XmlBuilder {
StringWriter writer = new StringWriter();
StreamResult result = new StreamResult(writer);
DOMSource source = new DOMSource(doc);
trans.setOutputProperty(OutputKeys.INDENT, "yes");
trans.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
trans.transform(source, result);
return writer.toString();
} catch (TransformerException e) {

12
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/word/WordBuilder.java
View File

@ -136,7 +136,11 @@ public class WordBuilder {
private void createPages(List<DatasetProfilePage> datasetProfilePages, XWPFDocument mainDocumentPart, Boolean createListing, VisibilityRuleService visibilityRuleService) {
datasetProfilePages.forEach(item -> {
try {
createSections(item.getSections(), mainDocumentPart, ParagraphStyle.HEADER4, 0, createListing, visibilityRuleService);
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
});
}
@ -258,7 +262,7 @@ public class WordBuilder {
}
return sb.toString();
} else if (comboboxType.equals("wordlist")) {
return field.getValue().toString();
return field.getValue() != null ? field.getValue().toString() : "";
}
}
case "booleanDecision":
@ -271,11 +275,9 @@ public class WordBuilder {
if (field.getValue() == null || field.getValue().equals("false")) return null;
return data.getLabel();
case "freetext":
return field.getValue().toString();
case "textarea":
return field.getValue().toString();
case "datepicker":
return field.getValue().toString();
case "textarea":
return field.getValue() != null ? field.getValue().toString(): "";
}
return null;
}

Some files were not shown because too many files have changed in this diff Show More