Method used to ingest data from PubMed SOAP interface. Brings in data as XML selected by either queries or record ranges and returns a stream of raw RDF/XML. Method can call a variety of fetch methods that allow selecting records based on a range of different attributes such as date added, date modified, number range, affiliation, etc.
To successfully harvest from PubMed:
- Model - vivo.xml should be configured to point to your chosen vivo.
- Task - create a pubmedfetch.xml (2 examples are provided).(Help for the search term)
- Datamap - pubmed-to-vivo.xsl currently maps the data to the UF implementation this will have to be adjusted.
Runs, sanitizes, and outputs the results of a EFetch request to the xmlWriter
- create a buffer
- connect to pubmed
- run the efetch request
- get the article set
- create XML writer
- output to buffer
- dump buffer to string
- use sanitizeXML on string
Sanitizes the XML in preparation for the output stream
- replaces the input characters
- writes to the output stream
- the OsWriter is provided in the superclass NIHFetch
Configuration file example