Draft
Page in draft form
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 the OS contains all the necessary commands to run the dspace2vivo scripts | Excute 'ls' command from $GIT_REPO DSpace-VIVO/releng/org.vivoweb.dspacevivo.installer/99-OTHER_TOOLS/validate-syscmd-config.sh adduser ok! ant ok! as ok! at ok! awk ok! basename ok! bash ok! cat ok! chmod ok! chown ok! chroot ok! clear ok! convert ok! cp ok! curl ok! cut ok! ... |
| 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 Demo-DSpace 6 (https://demo.dspace.org/jspui/) and DemoDSpace-7 (https://demo7.dspace.org/) 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. You can customize the harvesting settings according to the instructions in this section: Harvester Configuration
Start the migration from DSPace to VIVO
- make sure Solr and Tomcat are running (see Run - Start/Stop VIVO and Visual confirmation in your web browser)
- Compile ETL-migration program
Run migrating proccess
./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/script/mvn_install_example.sh
- Run ETL-Migration program
Run migrating proccess
./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/script/ETL-migration-DSpace-VIVO.sh
Sample result in VIVO after running the migration scripts
Harvester configuration
Once the migration environment has been configured as indicated in the previous steps, the migration process is executed. To execute this process, we proceed to configure the program with information from the harvest source (dspace).
This configuration is done in the harvest config file.
Config file path to configure Dspace source
./DSpace-VIVO/bundles/org.vivoweb.dspacevivo.transformation/src/main/resources/harvester.conf
In the file you will find an example of the fields that the configuration file should contain. At the moment two ways of harvesting the data are supported:
- OAI : It uses the OAI-PMH protocol supported by the Dspace repositories for information harvesting. Make sure you have an OAI-PMH endpoint enabled in the Dspace repository.
- Restv7 : It uses the Dspace APIs to query data. At the moment it is only compatible with versions of Dspace 7.
The following table shows the main fields that are required to configure the information harvesting process from dspace
| 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 |
Compile Harvester sources
Go to the following path.
Base directory of harvest components
./DSpace-VIVO/bundles/
Compile the project components
Maven compile command
mvn clean install
Install aditional components
Some migration processes are executed through bash scripts and require the installation of some special commands such as:
- sparql command: Allows you to perform sparql queries. to install it refer to the documentation in the following link : https://jena.apache.org/tutorials/sparql_query1.html
