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
./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/script/mvn_install_example.sh
- Run ETL-Migration program
./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/script/ETL-migration-DSpace-VIVO.sh
Sample result in VIVO after running the migration scripts
Customize the harvesting process
The initial harvesting process is configured to achieve a fast result. The configuration values can be adjusted to meet your experimental needs
Harvester configuration
To change the harvesting parameters of DemoDSpace6 and DemoDspace-7, edit and adjust the configuration values of the following two files:
./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/src/main/resources/harvester-dspace6.conf ./DSpace-VIVO/test/org.vivoweb.dspacevivo.etlexample/src/main/resources/harvester-dspace7.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/ |
harvestTotalCount | Number of items to harvest (proposed value = 5); put the parameter in comment to harvest all the site items | 5 |
username | User of the dspace platform with permissions to use the rest API. (RESTv7 Only). | admin |
password: | Password of the user (RESTv7 Only). | admin |
After the configuration as desired, simply restart the harvesting script as described: Run ETL-Migration program
Technical information
This section aims to present different technical aspects for an extended use of this example
Script directories
#!/bin/bash ################################################################### # Script Name : 00-env.sh # Description : This file is used to define the environment variables # needed to run the extract/transform/load (ETL) # process of dspace2vivo # Args : # Author : Michel Héon PhD # Institution : Université du Québec à Montréal # Copyright : Université du Québec à Montréal (c) 2022 # Email : heon.michel@uqam.ca ################################################################### # Scripts root directory export LOC_SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd -P)" ################################################################### # Root installation directory of the different dspace2vivo packages export INSTALLER_DIR=$(cd $LOC_SCRIPT_DIR/../../../releng/org.vivoweb.dspacevivo.installer ; pwd -P) ################################################################### # Project root variables source $INSTALLER_DIR/00-env.sh ################################################################### # Executable and script path needed to run dspace2VIVO PATH=$LOC_SCRIPT_DIR:$PATH ################################################################### # Working directory of scripts export WORKDIR=$(cd $LOC_SCRIPT_DIR/../; pwd -P) ################################################################### # Directory of resources needed to configure the expected operation of the scripts export RESSOURCESDIR=$(cd $WORKDIR/src/main/resources ; pwd -P) ################################################################### # Directory containing the correspondence files between DSpace values and VIVO values export MAPPING_DATA_DIR=$(cd $RESSOURCESDIR/mapping_data ; pwd -P) ################################################################### # Resource directories after compilation. This directory is modified at each compilation (Do not edit) export RESSOURCES_TARGET_DIR=$(cd $WORKDIR/target/classes ; pwd -P) ################################################################### # Directory containing the queries necessary for the execution of SPARQL export QUERY_DIR=$(cd $RESSOURCESDIR/query ; pwd -P) ################################################################### # Repositories containing transient data from the extract/transform/load process export DATA_DIR=$(cd $WORKDIR/data ; pwd -P) export DATA_DEMO6_DIR=$(cd $WORKDIR/data_src_dspace6 ; pwd -P) export DATA_DEMO7_DIR=$(cd $WORKDIR/data_src_dspace7 ; pwd -P) ################################################################### # Data transition sub-directories for each step of the ETL process export ETL_DIR_EXTRACT=$DATA_DIR/extract export ETL_DIR_TRANSFORM=$DATA_DIR/transform export ETL_DIR_TRANSFORM_DOC_TYPE=$(cd ${ETL_DIR_TRANSFORM}_doc_type ; pwd -P) export ETL_DIR_TRANSFORM_PERSON=$(cd ${ETL_DIR_TRANSFORM}_person ; pwd -P) export ETL_DIR_TRANSFORM_EXPERTISES=$(cd ${ETL_DIR_TRANSFORM}_expertises ; pwd -P) export ETL_DIR_TRANSFORM_PERSON_EXPERTISES=$(cd ${ETL_DIR_TRANSFORM}_person_expertises ; pwd -P)