Pubmed Efetch Bug

Question

[d.caliano]

Hi,

I'm using Pubmed Eutilities for Java to download a large set of articles. I First make a Esearch to download 1000 pubmed ids, then for each id I make a Efetch to get various information about the article, like the data, title, authors...

public static void fetchId(String id) {

EFetchPubmedServiceStub service = new EFetchPubmedServiceStub(); 
EFetchPubmedServiceStub.EFetchRequest req = new EFetchPubmedServiceStub.EFetchRequest();
req.setId(id); 
EFetchPubmedServiceStub.EFetchResult res = service.run_eFetch(req);

But for some ids (about 3/1000) I have a

org.apache.axis2.AxisFault
    at org.apache.axis2.AxisFault.makeFault(AxisFault.java:430)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub.fromOM(EFetchPubmedServiceStub.java:33767)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub.run_eFetch(EFetchPubmedServiceStub.java:189)
    at Searcher.fetchId2(Searcher.java:60)
    at Sistema.main(Sistema.java:17)
Caused by: java.lang.IllegalArgumentException
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$NlmCategory_type0$Factory.fromString(EFetchPubmedServiceStub.java:1636)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$NlmCategory_type0$Factory.fromString(EFetchPubmedServiceStub.java:1647)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$AbstractTextType$Factory.parse(EFetchPubmedServiceStub.java:24895)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$AbstractType$Factory.parse(EFetchPubmedServiceStub.java:59319)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$ArticleType$Factory.parse(EFetchPubmedServiceStub.java:11998)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$MedlineCitationType$Factory.parse(EFetchPubmedServiceStub.java:28780)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleType$Factory.parse(EFetchPubmedServiceStub.java:19147)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleSetChoiceE$Factory.parse(EFetchPubmedServiceStub.java:25376)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$PubmedArticleSet_type0$Factory.parse(EFetchPubmedServiceStub.java:56562)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub$EFetchResult$Factory.parse(EFetchPubmedServiceStub.java:50608)
    at gov.nih.nlm.ncbi.www.soap.eutils.EFetchPubmedServiceStub.fromOM(EFetchPubmedServiceStub.java:33761)

Do you know how to fix this?

[Pierre Lindenbaum]

do you really need to use the NCBI java binaries to fetch those pmid ?