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danro9685 / OncoScore

OncoScore is a tool to measure the association of genes to cancer based on citation frequency in biomedical literature. The manuscript of the method is published on Scientific Reports and available at http://www.nature.com/articles/srep46290.
https://danro9685.github.io/OncoScore/
GNU General Public License v3.0
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Error in get.list.from.xml(webget) #21

Closed robinjugas closed 2 years ago

robinjugas commented 2 years ago

Hello. I am getting two errors, somehow tied together. I am querying large number of genes and I got:

Warning: Number of items was greater than expected. PARTIAL RESULTS USED [MaxRet needs to be increased].

I discovered this is caused by gene named "TH". When I use perform.query("TH", gene.num.limit=100000) I got Error in get.list.from.xml(webget) : Warning: Number of items was different than the number of references.

I'll easily remove such a gene from a query. But it would be useful to handle this rare exception so it doesn't stop the whole query.

Thank you for the package anyway, it does the job really well. Regards, Robin

danro9685 commented 2 years ago

Dear @robinjugas,

Thanks for letting us know! I will close this issue as it seems you have fixed it from your side. We will handle this in the package.

Thanks, Daniele

pjlaw commented 7 months ago

Hi

I'm not sure if this is still being looked into but I'm getting the same error

query = perform.query(c("MYC"))
### Starting the queries for the selected genes.

### Performing queries for cancer literature 
Error in get.list.from.xml(webget) : 
  Warning: Number of items was different than the number of references.

I believe this is because this is a very well studied gene, so there are a lot of references being returned. In the get.list.from.xml function:

> lc = get.count.of.list(webget)
> lc
[1] 37877
> length(ListItems)
[1] 9999

From the ESearch documentation:

retmax Total number of UIDs from the retrieved set to be shown in the XML output (default=20). By default, ESearch only includes the first 20 UIDs retrieved in the XML output. If usehistory is set to 'y', the remainder of the retrieved set will be stored on the History server; otherwise these UIDs are lost. Increasing retmax allows more of the retrieved UIDs to be included in the XML output, up to a maximum of 10,000 records.

To retrieve more than 10,000 UIDs from databases other than PubMed, submit multiple esearch requests while incrementing the value of retstart (see Application 3). For PubMed, ESearch can only retrieve the first 10,000 records matching the query. To obtain more than 10,000 PubMed records, consider using that contains additional logic to batch PubMed search results automatically so that an arbitrary number can be retrieved.

So even through retmax is set to 3000000 in the code, ESearch will only return the first 10,000