ssl anomaly in pubmed dump

docs/Pubmed404.md

@@ -51,6 +51,11 @@ $ ./gradlew pubmed404
 
 The java jar file will be installed in the `dist` directory.
 
+
+## Creation Date
+
+20181210
+
 ## Source code 
 
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/Pubmed404.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/Pubmed404.java)
@@ -76,3 +81,41 @@ The current reference is:
 > Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare.
 > [http://dx.doi.org/10.6084/m9.figshare.1425030](http://dx.doi.org/10.6084/m9.figshare.1425030)
 
+
+## Example
+
+```
+$ java -jar dist/pubmeddump.jar 'bioinformatics 2001' 2> /dev/null |\
+	java -jar dist/pubmed404.jar  2> /dev/null 
+
+#PMID	TITLE	YEAR	URL	Status
+29520589	Expression of Colocasia esculenta tuber agglutinin in Indian mustard provides resistance against Lipaphis erysimi and the expressed protein is non-allergenic.2018	http://www.fao.org/docrep/007/y0820e/y0820e00.HTM	200
+29520589	Expression of Colocasia esculenta tuber agglutinin in Indian mustard provides resistance against Lipaphis erysimi and the expressed protein is non-allergenic.2018	http://www.icmr.nic.in/guide/Guidelines%20for%20Genetically%20Engineered%20Plants.pdf	-1
+28482857	Horizontal gene transfer is not a hallmark of the human genome.	2017	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0607-3	200
+27899642	The UCSC Genome Browser database: 2017 update.	2017	http://genome.ucsc.edu/	200
+27797935	High hospital research participation and improved colorectal cancer survival outcomes: a population-based study.	2017	http://www.bmj.com/company/products-services/rights-and-licensing/	403
+25505092	NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.	2015	http://pine.nmrfam.wisc.edu/download_packages.html	200
+25505092	NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.	2015	http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm	200
+25428374	The UCSC Genome Browser database: 2015 update.	2015	http://genome.ucsc.edu	200
+26356339	A Simple but Powerful Heuristic Method for Accelerating k-Means Clustering of Large-Scale Data in Life Science.	null	http://mlab.cb.k.u-tokyo.ac.jp/~ichikawa/boostKCP/	200
+24794704	Usefulness of the Shock Index as a secondary triage tool.	2015	http://group.bmj.com/group/rights-licensing/permissions	403
+24225322	Progenetix: 12 years of oncogenomic data curation.	2014	http://www.progenetix.org	200
+24137000	Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.	2014	http://globin.bx.psu.edu/hbvar	200
+24137000	Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.	2014	http://www.findbase.org	200
+24137000	Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.	2014	http://www.lovd.nl	200
+23564938	DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.	2013	http://dambe.bio.uottawa.ca	200
+22689647	SIFT web server: predicting effects of amino acid substitutions on proteins.	2012	http://sift-dna.org	200
+22600740	Cyber-T web server: differential analysis of high-throughput data.	2012	http://cybert.ics.uci.edu/	200
+21742331	An open source lower limb model: Hip joint validation.	2011	https://simtk.org/home/low_limb_london	200
+21593132	Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA.	2011	http://www.compbio.dundee.ac.uk/jabaws	200
+20228129	DensiTree: making sense of sets of phylogenetic trees.	2010	http://compevol.auckland.ac.nz/software/DensiTree/	404
+19380317	CELLULAR OPEN RESOURCE (COR): current status and future directions.	2009	http://www.cellml.org/specifications/	200
+18948284	OperonDB: a comprehensive database of predicted operons in microbial genomes.	2009	http://operondb.cbcb.umd.edu	200
+18368364	Simulator for neural networks and action potentials.	2007	http://snnap.uth.tmc.edu	-1
+18367465	An improved general amino acid replacement matrix.	2008	http://atgc.lirmm.fr/LG	404
+18238804	Interoperability with Moby 1.0--it's better than sharing your toothbrush!	2008	http://www.biomoby.org/	200
+18174178	PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.	2008	http://www.ibi.vu.nl/programs/pralinewww	200
+17221864	HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.	2007	http://globin.bx.psu.edu/hbvar	200
+17221864	HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.	2007	http://www.goldenhelix.org/xprbase	403
+(...)
+```

docs/PubmedDump.md

@@ -23,6 +23,9 @@ Usage: pubmeddump [options] Files
       java property file ${HOME}/.ncbi.properties and key api_key
     -o, --output
       Output file. Optional . Default: stdout
+    -r, --retmax
+      value for 'retmax' parameter for Eutils.
+      Default: 10000
     -skip, --skip
       [20180302]  Optional set of elements names to be ignored in the output. 
       Spaces or comma separated. .eg: 'AuthorList PubmedData '
@@ -64,6 +67,11 @@ $ ./gradlew pubmeddump
 
 The java jar file will be installed in the `dist` directory.
 
+
+## Creation Date
+
+20140805
+
 ## Source code 
 
 [https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedDump.java](https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedDump.java)

src/main/java/com/github/lindenb/jvarkit/io/IOUtils.java

@@ -259,8 +259,10 @@ public static byte[] gzipString(final String s) {
 		}
 	}
 
-	public static boolean isRemoteURI(String uri)
+	public static boolean isRemoteURI(final String uri)
 		{	
+		if(uri==null) return false;
+		if(!IOUtil.isUrl(uri)) return false;
 	    return  uri.startsWith("http://") ||
 				uri.startsWith("https://") ||
 				uri.startsWith("ftp://")

src/main/java/com/github/lindenb/jvarkit/tools/pubmed/Pubmed404.java

@@ -26,10 +26,10 @@ of this software and associated documentation files (the "Software"), to deal
 package com.github.lindenb.jvarkit.tools.pubmed;
 
 import java.io.ByteArrayInputStream;
-import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.PrintWriter;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.regex.Pattern;
@@ -62,6 +62,7 @@ of this software and associated documentation files (the "Software"), to deal
 import htsjdk.samtools.util.IOUtil;
 
 /**
+BEGIN_DOC
 
 ## Example
 
@@ -100,16 +101,18 @@ of this software and associated documentation files (the "Software"), to deal
 17221864	HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.	2007	http://www.goldenhelix.org/xprbase	403
 (...)
 ```
-
+END_DOC
 */
 @Program(name="pubmed404",
 description="Test if URL in the pubmed abstracts are reacheable.",
-keywords={"pubmed","url"}
+keywords={"pubmed","url"},
+creationDate="20181210",
+modificationDate="20200204"
 )
 public class Pubmed404  extends Launcher{
 	private static final Logger LOG = Logger.build(Pubmed404.class).make();
 	@Parameter(names={"-o","--output"},description=OPT_OUPUT_FILE_OR_STDOUT)
-	private File outFile=null;
+	private Path outFile=null;
 	@Parameter(names={"-t","--timeout"},description="timeout in seconds")
 	private int timeoutSeconds = 5;
 	@Parameter(names={"-c","--collapse"},description="Only one URL per article. Print the '200/OK' first.")
@@ -223,7 +226,7 @@ else if(eltName.equals(rootName))
 				token=token.substring(0,token.length()-1);
 			}
 			if(token.isEmpty()) continue;
-			if(!IOUtil.isUrl(token)) {
+			if(!IOUtils.isRemoteURI(token)) {
 				if(token.startsWith("http")) LOG.debug("strange url: "+token);
 				continue;
 			}
@@ -273,8 +276,6 @@ public int doWork(final List<String> args) {
 		InputStream in=null;
 		try {
 			/** create http client */
-
-
 			this.httpClient = HttpClients.createSystem();//createDefault();
 
 
@@ -290,7 +291,7 @@ public Object resolveEntity(String publicID, String systemID, String baseURI, St
 			in=(inputName==null?stdin():IOUtils.openURIForReading(inputName));
 			r = xmlInputFactory.createXMLEventReader(in);
 
-			out = super.openFileOrStdoutAsPrintWriter(this.outFile);
+			out = super.openPathOrStdoutAsPrintWriter(this.outFile);
 			out.println("#PMID\tTITLE\tYEAR\tURL\thttp.code\thttp.reason");
 
 			while(r.hasNext()) {
@@ -320,8 +321,7 @@ public Object resolveEntity(String publicID, String systemID, String baseURI, St
 
 		}
 
-public static void main(final String[] args)
-	{
+public static void main(final String[] args) {
 	new Pubmed404().instanceMainWithExit(args);
 	}
 }