Summary
Introduction
This page presents the procedure for migrating data from DSpace to VIVO. It answers the use case of a VIVO instance in read-only mode used to present the metadata contained in DSpace
Goals
- The scenario to be realized by this procedure consists in developing the necessary steps in order to migrate the metadata of two DSpace instances (the DSpace-6 Demo instance and the DSpace-7 Demo instance) to a local VIVO instance
- At the end of this procedure, the experimenter should have a fully operational VIVO instance containing the metadata harvested from DSpace-6-Demo DSpace-7-Demo, both of which are available from the web.
- The experimenter will also have in his possession, the necessary information to harvest in VIVO the metadata of a DSpace instance that he will have chosen and that it is possible to harvest from an OAI-PMH endpoint
Useful addresses
Title | URL | Description |
---|---|---|
DSpace-6 Demo Home Page | This entry page links to other links concerning the DSpace-6 demo | |
DSpace-6 Demo UI | https://demo.dspace.org/xmlui/ | This page is the DSpace-6 api allowing to manipulate metadata |
DSpace-6 OAI Api | https://demo.dspace.org/oai/request | OAI API used to harvest data |
DSpace-7 Demo Home Page | https://demo7.dspace.org/home | This entry page links to other links concerning the DSpace-7 demo |
VIVO Project GitHub Home Page | https://github.com/vivo-project | Source code location needed to install VIVO |
DSpace-VIVO Integration Project (DV-IP) | https://github.com/vivo-community/DSpace-VIVO | Source code location for the migration of DSpace metadata to VIVO |
DSpace-VIVO ETL Example | https://github.com/vivo-community/DSpace-VIVO/tree/main/test/org.vivoweb.dspacevivo.etlexample | Source code location for extract-transform-load (ETL) metadata processing from DSpace to VIVO |
Useful variable and constant names
Title | Var Name | Var Value | Description |
---|---|---|---|
Project root directory | DVIP_HOME_PRJ | ~/dspace-vivo-prj | The value content is a suggestion |
Git root directory | GIT_REPO | $DVIP_HOME_PRJ/00-GIT | Directory containing extracted GIT projects |
Default VIVO login (username - password) | admin@vivo.org | Vivo1234. | To be used to log-in as a VIVO administrator |
local server URLs | SOLR | http://localhost:8983/solr/#/ | |
VIVO | http://localhost:8080/vivo-dspace/ |
Software requirements
- jdk 11
- maven 3.6.3
- Linux Ubuntu
- No solr or tomcat instance should be running on the computer
- Linux bash
Setting up
Setting up the necessary resources for running VIVO
Step name and description | Commands |
---|---|
Setting up project | mkdir -p ~/dspace-vivo-prj/00-GIT |
Retrieve the DV-IP source code | git clone https://github.com/vivo-community/DSpace-VIVO |
Install Solr + Tomcat | ./DSpace-VIVO/releng/org.vivoweb.dspacevivo.installer/00-INIT/install-tomcat-solr-app.sh |
Installing/compiling VIVO | ./DSpace-VIVO/releng/org.vivoweb.dspacevivo.installer/01-VIVO/vivo-git-clone.sh ./DSpace-VIVO/bundles/org.vivoweb.dspacevivo/script/vivo-compile-and-deploy-for-tomcat.sh |
Run - Start/Stop VIVO | Starting VIVO source ./DSpace-VIVO/bundles/org.vivoweb.dspacevivo/script/00-env.sh solr-start.sh tomcat-start.sh To show VIVO in a Web Browser browse-vivo.sh For stopping VIVO tomcat-stop.sh solr-stop.sh |
Setting up the necessary resources for running Dspace
TODO
Installing the migration utilities
Step name and description | Commands |
---|---|
Install Apache Jena and its other associated tools | ./DSpace-VIVO/releng/org.vivoweb.dspacevivo.installer/99-OTHER_TOOLS/jena-git-clone-and-deploy.sh |
Compiling/Installing DSpace-VIVO-EXEMPLE and its code libraries | ./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/script/mvn_install_example.sh |
Confirm the installation
The purpose of this step is to validate the correct installation of the components necessary for the scenario to proceed. Here is a series of command that can be executed along with their execution result allowing you to compare them with the result of your own installation
Step name and description | Commands |
---|---|
Validate that all necessary GIT projects are cloned and properly deployed | Excute 'ls' command from $GIT_REPO ls -l total 24 drwxrwxr-x 6 heon heon 4096 mai 20 14:04 data-format-translator drwxrwxr-x 7 heon heon 4096 mai 20 11:02 DSpace-VIVO drwxrwxr-x 9 heon heon 4096 mai 20 11:08 Vitro drwxrwxr-x 11 heon heon 4096 mai 20 11:08 Vitro-languages drwxrwxr-x 10 heon heon 4096 mai 20 11:08 VIVO drwxrwxr-x 11 heon heon 4096 mai 20 11:08 VIVO-languages Execute 'ls' from $GIT_REPO in deploy directory ls -dl ./DSpace-VIVO/deploy/*/ drwxrwxr-x 9 heon heon 4096 mai 20 11:07 ./DSpace-VIVO/deploy/app-solr/ drwxrwxr-x 9 heon heon 4096 mai 20 11:07 ./DSpace-VIVO/deploy/app-tomcat/ drwxrwxr-x 2 heon heon 4096 mai 20 14:05 ./DSpace-VIVO/deploy/lib/ drwxrwxr-x 7 heon heon 4096 mai 20 14:04 ./DSpace-VIVO/deploy/translator/ drwxrwxr-x 9 heon heon 4096 mai 20 11:13 ./DSpace-VIVO/deploy/vivo-home/ |
Test the utilities to make sure they are working | Setting up environment variables in your session (From $GIT_REPO) $ source DSpace-VIVO/bundles/org.vivoweb.dspacevivo/script/00-env.sh Validate Solr $ solr-start.sh Waiting up to 180 seconds to see Solr running on port 8983 [|] Started Solr server on port 8983 (pid=1741315). Happy searching! $ solr-status.sh Found 1 Solr nodes: Solr process 56366 running on port 8983 { "solr_home":"xxxxxxx/00-GIT/DSpace-VIVO/deploy/app-solr/server/solr", "version":"8.11.1 0b002b11819df70783e83ef36b42ed1223c14b50 - janhoy - 2021-12-14 13:50:55", "startTime":"2022-05-19T15:15:10.534Z", "uptime":"0 days, 17 hours, 25 minutes, 10 seconds", "memory":"151 MB (%29.5) of 512 MB"} Validate Tomcat $ tomcat-start.sh Using CATALINA_BASE: xxxxxxx/00-GIT/DSpace-VIVO/deploy/app-tomcat Using CATALINA_HOME: xxxxxxx/00-GIT/DSpace-VIVO/deploy/app-tomcat Using CATALINA_TMPDIR: xxxxxxx/00-GIT/DSpace-VIVO/deploy/app-tomcat/temp Using JRE_HOME: /opt/jdk-11.0.9 Using CLASSPATH: xxxxxxx/00-GIT/DSpace-VIVO/deploy/app-tomcat/bin/tomcat-juli.jar Using CATALINA_OPTS: Tomcat started. Test Apache-Jena $ sparql -version 2>/dev/null Jena: VERSION: 3.17.0 Jena: BUILD_DATE: 2020-11-25T19:40:23+0000 |
Visual confirmation in your web browser
Visual of Solr | Visual for VIVO-DSpace |
---|---|
URL = http://localhost:8983/solr/#/ | URL = http://localhost:8080/vivo-dspace/ |
Migrate data from DSpace6-Demo and DSpace-7-Demo into VIVO with default migration values
- This scenario performs the DSpace Items reading of the DSpace 6 and 7 demonstration sites.
- In order to achieve a complete extraction in a respectable time, the data harvesting parameters are pre-programmed to import 5 Items per demonstration site for a total of 10 Items.
General Esquema
The migration process consists of 3 main phases as shown in the image :
Extraction : Harvest the Dspace repository to extract resources metadata
Transformation : The extracted data is mapped to a vocabulary compatible with the VIVO ontological model
Insertion: Insert the data as triples in the VIVO repository through its sparql API
Each of the phases is described below with the programs that are required to be executed to complete these tasks.
Extraction Phase
This phase begins the data migration process from Dspace to the VIVO platform. Make sure you have an instance of Dspace and VIVO running. To successfully complete this phase follow these steps :
Download the .jar file from the following link http:link_demo
Generate a config file with source dspace params:
Params Description Example type Type of API used for data extraction. Enable for now ( OAI, RESTv7 ) OAI endpoint API url direction. If the OAI type was selected, place the route of the OAI endpoint. On the other hand, if RESTv7 was selected, the rest API address. https://api7.dspace.org/server/oai/request uriPrefix The prefix of the link to the repository. Used to generate valid links to the source repository. https://demo7.dspace.org/ username User of the dspace platform with permissions to use the rest API. (RESTv7 Only). admin password: Password of the user (RESTv7 Only). admin Execute the java program with the config file path.
Run java executable to harvest dspace itemsjava jar vivo "/path_to_config_file/config_file.config"
Start the migration from DSPace to VIVO
- make sure Solr and Tomcat are running
./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/script/ETL-migration-DSpace-VIVO.sh