PubmedFetch

[trajkumarkvp]

Caused by: java.lang.ClassNotFoundException: org.vivoweb.harvester.fetch.nih.PubmedFetch

Dear Experts

How to solve this issue

[chenejac]

@trajkumarkvp can you please try to describe the bug in the following format.

Describe the bug A clear and concise description of what the bug is.

To Reproduce Steps to reproduce the behavior:

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Expected behavior A clear and concise description of what you expected to happen.

Screenshots If applicable, add screenshots to help explain your problem.

Environment (please complete the following information):

• OS: [e.g. Windows, Linux]
• Tomcat version [e.g. 8, 9]
• VIVO version [e.g. 1.11.0, 1.12.0]
• Apache Solr or ElasticSearch version

Additional context Add any other context about the problem here.

[trajkumarkvp]

Dear Expert: Can you please suggest which is the best vivo-harvester for VIVO 1.12.0

[chenejac]

I think you should fetch the last version from the main branch. Please, register for the VIVO slack channel at http://bit.ly/vivo-slack. There might be some VIVO implementers who struggled with similar issues in the past.

[trajkumarkvp]

Environment

• OS: Ubuntu 20.04

• Tomcat Version: 9

• VIVO Version: V.1.12.0

• Apache Solr or ElasticSearch version: Not Installed

• Installation

• I have installed VIVO 1.12.0 successfully

Expectations from the Experts

• How to install and configure the VIVO-harvester
• I have tried many times but I, could not configure properly

Dear experts please do the needful

[trajkumarkvp]

I think you should fetch the last version from the main branch. Please, register for the VIVO slack channel at http://bit.ly/vivo-slack. There might be some VIVO implementers who struggled with similar issues in the past.

Thank you so much for your prompt response and guidance.

[chenejac]

@trajkumarkvp VIVO can't be run without search engine (Solr by default) - https://wiki.lyrasis.org/display/VIVODOC112x/Installing+VIVO#InstallingVIVO-ConfigureandStartSolr

[trajkumarkvp]

@trajkumarkvp VIVO can't be run without search engine (Solr by default) - https://wiki.lyrasis.org/display/VIVODOC112x/Installing+VIVO#InstallingVIVO-ConfigureandStartSolr

Dear Expert, As per your instruction, I have installed solr version 8.11.2 in our VIVO version 1.12.0. Can you please help me to install and configure the harvester.

[trajkumarkvp]

root@ubuntu:/# /usr/share/vivo/harvester/example-scripts/example-pubmed/run-pubmed.sh Full Logging in example-pubmed.2023-05-01T05:43:45.log Unrecognized option: -d64 Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

Dear Experts, I have installed vivo-harvester 1.5. When, I start to fetch the pubmed data i am facing the above error. Can anyone please solve this issue.