Activity for GNAT
-
Kuni Katsuya modified a comment on ticket #4
I took a quick look at the code and the XML for PMID 20832752 and the expected format still appears to be valid: PubmedArticle MedlineCitation Article ArticleTitle Abstract AbstractText Hard to say what's causing the JDomParseException without throwing a debugger on it. Is there any chance of resurrecting the build script? :)
-
I took a quick look at the code and the XML for PMID 20832752 and the expected format still appears to be valid: PubmedArticle MedlineCitation Article ArticleTitle Abstract AbstractText Hard to say what's causing the JDomParseException without throwing a debugger on it. Is there any chance of resurrecting the build script? :)
-
On http://localhost:8081/?pmid=20832752&task=gner , the error: org.jdom.input.JDOMParseException: Error on line 1: White spaces are required between publicId and systemId. at org.jdom.input.SAXBuilder.build(SAXBuilder.java:468) at org.jdom.input.SAXBuilder.build(SAXBuilder.java:851) at gnat.retrieval.PubmedAccess.getAbstractsAsTitleAndTextFromXML(PubmedAccess.java:152) at gnat.retrieval.PubmedAccess.getAbstractsAsTitleAndText(PubmedAccess.java:95) at gnat.server.GnatServiceHandler.getTexts(GnatService.java:381)...
-
Jörg Hakenberg posted a comment on ticket #4
I believe NHI's PubMed XML output might have changed, that's why we're getting the Exception. We don't have a build script :( --- what errors are you getting?
-
Hi Jörg, I'm trying to debug the above JDOMParseException, but I am unable to compile the GNAT source. Is there a build file or script (e.g. Maven pom.xml, Ant build.xml, etc.) that I can use? Thanks
-
On a related note... When I got GnatService running with the above changes, I was able to successfully see the help page at http://localhost:8081. However, when I try http://localhost:8081/?pmid=20832752&task=gner, I get the following error: org.jdom.input.JDOMParseException: Error on line 1: White spaces are required between publicId and systemId. at org.jdom.input.SAXBuilder.build(SAXBuilder.java:468) at org.jdom.input.SAXBuilder.build(SAXBuilder.java:851) at gnat.retrieval.PubmedAccess.getAbstractsAsTitleAndTextFromXML(PubmedAccess.java:152)...
-
Cool, thanks, Jörg!
-
GnatService.sh won't start
-
Thanks for filing this issue. Let me take a look and update the binary downloads + example scripts.
-
GnatService.sh won't start
-
Thanks for pointing this out! I committed a code fix to Sourceforge but still need to generate new binaries for people to download if they are not working off the source code. Thanks again, Joerg On Sat, Nov 18, 2017 at 6:35 PM, Kuni Katsuya kczi@users.sf.net wrote: [tickets:#3] https://sourceforge.net/p/gnat/tickets/3/ NullPointerException from TextProcessor.getEnglishWordTokens()* Status: open Milestone: 1.0 Labels: bug Created: Sun Nov 19, 2017 02:35 AM UTC by Kuni Katsuya Last Updated: Sun Nov...
-
NullPointerException from TextProcessor.getEnglishWordTokens()
-
NullPointerException from TextProcessor.getEnglishWordTokens()
-
Fixed in source code; still need to re-up new binaries.
-
getEnglishWordTokens would throw an exception when the text was NULL: in this case, from a DB entry for a gene that simply had no Entrez Gene Summary, that is, the gene did exist but the value for 'summary' was NULL in the DB.
-
NullPointerException from TextProcessor.getEnglishWordTokens()
-
GNAT released /data/gnat_sql_data-1.5.tar.gz
-
Small changes in command line options.
-
Number of black-list terms was calculated based on lines in data/blacklists.txt. New version splits at '|' for counting & reporting. The actual processing was not affected, just the INFO message on the console.
-
Fixed an issue where abstracts that contain line breaks where not handled properly: a gene mention could have a [\r\n] in the middle, which messes up the final output etc.
-
-
Disambiguate gene mentions using already normalized genes from the same text
-
Disambiguate gene mentions using already normalized genes from the same text
-
Converting numerals larger than MAX INT found in a text
-
Blacklist for unlikely gene names in data/black...
-
-
-
-
-
-
-
New features
-
Sync'ing new libs.
-
Switching to NCBI HTTPS protocol. HTTP calls re...
-
Switching to NCBI HTTPS protocol. HTTP calls re...
-
-
Switching to NCBI HTTPS protocol. HTTP calls re...
-
Switching to NCBI HTTPS protocol. HTTP calls re...
-
-
-
-
-
-
Worked on parsing Medline XML using XPath.
-
-
Worked on the passphrase to stop a running serv...
-
Improved filters based on latest Medline results.
-
Added a method to Context to return a list of i...
-
Filename for go2go.obj now in isgnproperties.xml
-
-
New features
-
Home
-
TODO list
-
-
-
-
-
First version of an Annotator that reads single...
-
Getting rid of some Java Warnings.
-
Installation instructions
-
Home
-
-
-
'?' was missing from characters that need to be...
-
Error escaping the shortForm to form patterns t...
-
Corrected type in name of function StringHelper...
-
-
-
-
-
New binary release 1.3
-
New human dictionaries
-
New binary release 1.3
-
-
-
-
-
Binary release 1.3.
-
Added some FPs that often arise after convertin...
-
-
-
Added example script to stop a running dictiona...
-
-
Warnings go to STDERR now. Level: 'WARNINGS' an...
-
Work in progress: add methods to let the user u...
-
-
New MySQL JAR. (v5.1.28).
-
New MySQL JAR. (v5.1.28).
-
New MySQL JAR. (v5.1.28).
-
Cleanup. Removed or suppressed warnings (mostly...
-
Cleanup. Added SuppressWarning to uncalled cons...
-
Added a quick test for deployment/function of a...
-
Work in progress: add methods to let the user u...
-
Allow command line access to PubmedAccess. Firs...
-
PubMed2GO file can be gzipped now.
-
Working on a new data release
-
-
-
-
1 >