Comments (3)
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.
from vivo-harvester.
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:
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
from vivo-harvester.
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
from vivo-harvester.
Related Issues (20)
- Update pubmed-to-vivo.xsl to the new 1.6 Ontology
- Update dsr-to-vivo.xsl to the VIVO 1.6 Format
- Update the peoplesoft-to-vivo.datamap.xsl to the VIVO 1.6 format
- Modify score-* in courses for 1.6
- Modify score-* in pubmed for 1.6
- Modify score-* in peoplesoft for 1.6
- Modify score-* in dsr for 1.6 ontology
- Seperate the Example files for 1.5 and early and 1.6 and later HOT 1
- Review PubMed Excecution for more 1.6 changes
- Review Courses for more 1.6 Changes
- Review Peoplesoft Script for more 1.6 Changes
- Review DSR for more 1.6 Changes
- Replace all PubmedFetch by PubmedHTTPFetch?
- VIVO Harvester (xsltranslator issue) HOT 5
- OAI-FETCH error 302 ? HOT 1
- Request for guide HOT 7
- PubmedFetch HOT 8
- Add harvesting script for OpenAlex
- Add harvesting script for ConfIDent conference metadata
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from vivo-harvester.