Is VIVO_Harvester_(vivo.sourceforge.net) tool "decomisioned"?

[jcabrerazuniga]

While using the vivo harvester it is specified as a tool VIVO_Harvester_(vivo.sourceforge.net) as with:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?&db=pubmed&tool=VIVO_Harvester_(vivo.sourceforge.net) ....

but I am getting error messages that force me to ask if this VIVO_Harvester_(vivo.sourceforge.net) tool is still available or if it has been replaced by something better.
Also, the next link does not work anymore:
https://github.com/vivo-community/VIVO-Harvester/tree/develop

[gneissone]

The VIVO Harvester is not under active development, however it is still in use by some institutions. Can you please provide some more detail as to how you are trying to use the Harvester? It includes a suite of different tools and scripts. Are you trying to follow documentation provided somewhere?

I assume the broken link you mentioned is in the VIVO wiki. The correct branch is now 'main.' I updated the docs, thank you.

[jcabrerazuniga]

This starts at the moment the

harvester-pubmedhttpfetch

script is executed. This one calls:

harvester-pubmedhttpfetch -X pubmedfetch.config.xml

Our pubmedfetch.config.xml content is:

<?xml version="1.0" encoding="UTF-8"?>
<!--
  Copyright (c) 2010-2011 VIVO Harvester Team. For full list of contributors, please see the AUTHORS file provided.
  All rights reserved.
  This program and the accompanying materials are made available under the terms of the new BSD license which accompanies this distribution, and is available at http://www.opensource.org/licenses/bsd-license.html
-->
<Task >
   <Param name="wordiness">INFO</Param>
   <Param name="email">[email protected]</Param>
   <Param name="termSearch">4293524</Param>
   <Param name="numRecords">ALL</Param>
   <Param name="batchSize">1000</Param>
   <Param name="output">raw-records.config.xml</Param>
</Task>

So, the code calls:

java $OPTS -Dprocess-task=PubmedHTTPFetch org.vivoweb.harvester.fetch.nih.PubmedHTTPFetch "$@"

and this code calls PubMedHTTPFetch.java

that uses a link like:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?&db=pubmed&tool=VIVO_Harvester_(vivo.sourceforge.net) ....

and I get an error message like:

<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
<eSearchResult>
      <ERROR>Empty term and query_key - nothing todo</ERROR>
</eSearchResult>

if I run

wget -O wgetout.txt https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?&db=pubmed&tool=VIVO_Harvester_%28vivo.sourceforge.net%29&[email protected]&usehistory=y&retmode=xml&term=%5Bpmid%5D

I replaced the real email with someEmail.

Thanks
Jose

[trajkumarkvp]

The VIVO Harvester is not under active development, however it is still in use by some institutions. Can you please provide some more detail as to how you are trying to use the Harvester? It includes a suite of different tools and scripts. Are you trying to follow documentation provided somewhere?

I assume the broken link you mentioned is in the VIVO wiki. The correct branch is now 'main.' I updated the docs, thank you.

Dear Sir/Madam, I have tried many times to install the harverster but have some issues. kindly help me