Re: RFP for bioperl's Bio-EUtilities

To: Andreas Tille <andreas@an3as.eu>
Cc: "Fields, Christopher J" <cjfields@illinois.edu>, "debian-perl@lists.debian.org" <debian-perl@lists.debian.org>, "852004@bugs.debian.org" <852004@bugs.debian.org>, Debian Med <debian-med@lists.debian.org>
Subject: Re: RFP for bioperl's Bio-EUtilities
From: Carnë Draug <carandraug+dev@gmail.com>
Date: Thu, 26 Jan 2017 18:12:41 +0000
Message-id: <[🔎] CAPOrs_26x1vJJNzBX69+9mzYZ_-YhM2fzLvYdOf1T9x=Z8yBew@mail.gmail.com>

I have attached a git patch which adds a quilt patch to the repos.
This change inlines the DTDs in the xml files and pdebuild now
succeeds.

If this change fixes it for debian, we can apply it upstream.

Carnë

From 38a2038d0da47f6ac6b853b20b2934260257381d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Carn=C3=AB=20Draug?= <carandraug+dev@gmail.com>
Date: Thu, 26 Jan 2017 18:01:49 +0000
Subject: [PATCH] Inline DTDs on XML files required for testsuite so no
 internet is necessary

---
 debian/patches/inline-DTDs-on-testsuite | 948 ++++++++++++++++++++++++++++++++
 debian/patches/series                   |   1 +
 2 files changed, 949 insertions(+)
 create mode 100644 debian/patches/inline-DTDs-on-testsuite
 create mode 100644 debian/patches/series

diff --git a/debian/patches/inline-DTDs-on-testsuite b/debian/patches/inline-DTDs-on-testsuite
new file mode 100644
index 0000000..589c51c
--- /dev/null
+++ b/debian/patches/inline-DTDs-on-testsuite
@@ -0,0 +1,948 @@
+Index: libbio-eutilities-perl/t/data/eutils/egquery.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/egquery.xml
++++ libbio-eutilities-perl/t/data/eutils/egquery.xml
+@@ -1,11 +1,21 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE Result PUBLIC "-//NLM//DTD eSearchResult, January 2004//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/egquery.dtd";>
+-
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE Result [
++<!--
++        This is the Current DTD for Entrez eGSearch
++        $Id: egquery.dtd 39250 2004-05-03 16:19:48Z yasmax $
++--><!-- ================================================================= --><!ELEMENT DbName (#PCDATA)>
++<!-- .+ --><!ELEMENT MenuName (#PCDATA)>
++<!-- .+ --><!ELEMENT Count (#PCDATA)>
++<!-- \d+ --><!ELEMENT Status (#PCDATA)>
++<!-- .+ --><!ELEMENT Term (#PCDATA)>
++<!-- .+ --><!ELEMENT ResultItem (DbName , MenuName , Count , Status)>
++<!ELEMENT eGQueryResult (ResultItem)+>
++<!ELEMENT Result (Term , eGQueryResult)>
++]>
+ <!--
+         $Id: egquery_template.xml 106311 2007-06-26 14:46:31Z osipov $
+ -->
+ <!-- ================================================================= -->
+-
+ <Result>
+ 
+         <Term>Notch AND Mus musculus</Term>
+Index: libbio-eutilities-perl/t/data/eutils/einfo.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/einfo.xml
++++ libbio-eutilities-perl/t/data/eutils/einfo.xml
+@@ -1,5 +1,35 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD eInfoResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eInfoResult [
++<!--    
++                This is the Current DTD for Entrez eInfo
++$Id: eInfo_020511.dtd 393292 2013-03-22 21:30:47Z fialkov $
++--><!-- ================================================================= --><!ELEMENT DbName (#PCDATA)>
++<!-- \S+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT FullName (#PCDATA)>
++<!-- .+ --><!ELEMENT Description (#PCDATA)>
++<!-- .+ --><!ELEMENT DbBuild (#PCDATA)>
++<!-- .+ --><!ELEMENT TermCount (#PCDATA)>
++<!-- \d+ --><!ELEMENT Menu (#PCDATA)>
++<!-- .+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT MenuName (#PCDATA)>
++<!-- .+ --><!ELEMENT Count (#PCDATA)>
++<!-- \d+ --><!ELEMENT LastUpdate (#PCDATA)>
++<!-- \d+ --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT IsDate (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsNumerical (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT SingleToken (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT Hierarchy (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsHidden (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsRangable (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsTruncatable (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT DbList (DbName)+>
++<!ELEMENT Field (Name , FullName , Description , TermCount , IsDate , IsNumerical , SingleToken , Hierarchy , IsHidden , IsRangable? , IsTruncatable?)>
++<!ELEMENT Link (Name , Menu , Description , DbTo)>
++<!ELEMENT LinkList (Link)*>
++<!ELEMENT FieldList (Field)*>
++<!ELEMENT DbInfo (DbName , MenuName , Description , DbBuild? , Count , LastUpdate , FieldList , LinkList?)>
++<!ELEMENT eInfoResult (DbList | DbInfo | ERROR)>
++]>
+ <eInfoResult>
+ <DbInfo>
+ 	<DbName>pubmed</DbName>
+Index: libbio-eutilities-perl/t/data/eutils/einfo_dbs.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/einfo_dbs.xml
++++ libbio-eutilities-perl/t/data/eutils/einfo_dbs.xml
+@@ -1,5 +1,35 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eInfoResult PUBLIC "-//NLM//DTD eInfoResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eInfo_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eInfoResult [
++<!--    
++                This is the Current DTD for Entrez eInfo
++$Id: eInfo_020511.dtd 393292 2013-03-22 21:30:47Z fialkov $
++--><!-- ================================================================= --><!ELEMENT DbName (#PCDATA)>
++<!-- \S+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT FullName (#PCDATA)>
++<!-- .+ --><!ELEMENT Description (#PCDATA)>
++<!-- .+ --><!ELEMENT DbBuild (#PCDATA)>
++<!-- .+ --><!ELEMENT TermCount (#PCDATA)>
++<!-- \d+ --><!ELEMENT Menu (#PCDATA)>
++<!-- .+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT MenuName (#PCDATA)>
++<!-- .+ --><!ELEMENT Count (#PCDATA)>
++<!-- \d+ --><!ELEMENT LastUpdate (#PCDATA)>
++<!-- \d+ --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT IsDate (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsNumerical (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT SingleToken (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT Hierarchy (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsHidden (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsRangable (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT IsTruncatable (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT DbList (DbName)+>
++<!ELEMENT Field (Name , FullName , Description , TermCount , IsDate , IsNumerical , SingleToken , Hierarchy , IsHidden , IsRangable? , IsTruncatable?)>
++<!ELEMENT Link (Name , Menu , Description , DbTo)>
++<!ELEMENT LinkList (Link)*>
++<!ELEMENT FieldList (Field)*>
++<!ELEMENT DbInfo (DbName , MenuName , Description , DbBuild? , Count , LastUpdate , FieldList , LinkList?)>
++<!ELEMENT eInfoResult (DbList | DbInfo | ERROR)>
++]>
+ <eInfoResult>
+ <DbList>
+ 	<DbName>pubmed</DbName>
+Index: libbio-eutilities-perl/t/data/eutils/elink_acheck.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_acheck.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_acheck.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_acheck_corr.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_acheck_corr.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_acheck_corr.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_dball.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_dball.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_dball.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_lcheck.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_lcheck.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_lcheck.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_lcheck_corr.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_lcheck_corr.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_lcheck_corr.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_llinks.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_llinks.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_llinks.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_llinks_corr.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_llinks_corr.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_llinks_corr.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_multidb.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_multidb.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_multidb.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_multidb_corr.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_multidb_corr.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_multidb_corr.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_ncheck.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_ncheck.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_ncheck.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_ncheck_corr.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_ncheck_corr.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_ncheck_corr.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_neighbor.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_neighbor.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_neighbor.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_neighbor_corr.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_neighbor_corr.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_neighbor_corr.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_nhist.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_nhist.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_nhist.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_nhist_corr.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_nhist_corr.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_nhist_corr.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/elink_scores.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/elink_scores.xml
++++ libbio-eutilities-perl/t/data/eutils/elink_scores.xml
+@@ -1,5 +1,34 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eLinkResult [
++<!--    
++                This is the Current DTD for Entrez eLink
++$Id: eLink_020511.dtd 56256 2005-02-18 17:13:40Z olegh $
++--><!-- ================================================================= --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT Info (#PCDATA)>
++<!-- .+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ATTLIST Id HasLinkOut (Y | N) #IMPLIED>
++<!ATTLIST Id HasNeighbor (Y | N) #IMPLIED>
++<!ELEMENT Score (#PCDATA)>
++<!-- \d+ --><!ELEMENT DbFrom (#PCDATA)>
++<!-- \S+ --><!ELEMENT DbTo (#PCDATA)>
++<!-- \S+ --><!ELEMENT LinkName (#PCDATA)>
++<!-- \S+ --><!ELEMENT IdList (Id)*>
++<!-- cmd=neighbor --><!ELEMENT Link (Id , Score?)>
++<!ELEMENT LinkSetDb (DbTo , LinkName , (Link* | Info) , ERROR?)>
++<!-- cmd=links --><!ELEMENT Url (#PCDATA)>
++<!-- \S+ --><!ELEMENT IconUrl (#PCDATA)>
++<!-- \S+ --><!ELEMENT SubjectType (#PCDATA)>
++<!-- .+ --><!ELEMENT Attribute (#PCDATA)>
++<!-- .+ --><!ELEMENT Name (#PCDATA)>
++<!-- .+ --><!ELEMENT NameAbbr (#PCDATA)>
++<!-- \S+ --><!ELEMENT Provider (Name , NameAbbr , Id , Url , IconUrl?)>
++<!ELEMENT ObjUrl (Url , IconUrl? , LinkName? , SubjectType* , Attribute* , Provider)>
++<!ELEMENT IdUrlSet (Id , (ObjUrl+ | Info))>
++<!ELEMENT IdUrlList (IdUrlSet* , ERROR?)>
++<!-- cmd=ncheck & lcheck --><!ELEMENT IdCheckList (Id* , ERROR?)>
++<!-- Common --><!ELEMENT LinkSet (DbFrom , ((IdList? , LinkSetDb*) | IdUrlList | IdCheckList | ERROR))>
++<!ELEMENT eLinkResult (LinkSet* , ERROR?)>
++]>
+ <eLinkResult>
+ <LinkSet>
+ 	<DbFrom>protein</DbFrom>
+Index: libbio-eutilities-perl/t/data/eutils/epost.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/epost.xml
++++ libbio-eutilities-perl/t/data/eutils/epost.xml
+@@ -1,5 +1,15 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE ePostResult PUBLIC "-//NLM//DTD ePostResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE ePostResult [
++<!--    
++                This is the Current DTD for Entrez ePost
++$Id: ePost_020511.dtd 161288 2009-05-26 18:34:21Z fialkov $
++--><!-- ================================================================= --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ELEMENT InvalidIdList (Id)+>
++<!ELEMENT QueryKey (#PCDATA)>
++<!-- \d+ --><!ELEMENT WebEnv (#PCDATA)>
++<!-- \S+ --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT ePostResult (InvalidIdList? , (QueryKey , WebEnv)? , ERROR?)>
++]>
+ <ePostResult>
+ 	<QueryKey>1</QueryKey>
+ 	<WebEnv>0rACq8_iP87yHkqqm0SBaU38LzWLHIUd-J4QozMr31bh_XO5KAxLr5Q0o2e@03ED1E11941B69F1_0100SID</WebEnv>
+Index: libbio-eutilities-perl/t/data/eutils/esearch1.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/esearch1.xml
++++ libbio-eutilities-perl/t/data/eutils/esearch1.xml
+@@ -1,5 +1,36 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eSearchResult [
++<!--    
++                This is the Current DTD for Entrez eSearch
++$Id: eSearch_020511.dtd 85163 2006-06-28 17:35:21Z olegh $
++--><!-- ================================================================= --><!ELEMENT Count (#PCDATA)>
++<!-- \d+ --><!ELEMENT RetMax (#PCDATA)>
++<!-- \d+ --><!ELEMENT RetStart (#PCDATA)>
++<!-- \d+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ELEMENT From (#PCDATA)>
++<!-- .+ --><!ELEMENT To (#PCDATA)>
++<!-- .+ --><!ELEMENT Term (#PCDATA)>
++<!-- .+ --><!ELEMENT Field (#PCDATA)>
++<!-- .+ --><!ELEMENT QueryKey (#PCDATA)>
++<!-- \d+ --><!ELEMENT WebEnv (#PCDATA)>
++<!-- \S+ --><!ELEMENT Explode (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT OP (#PCDATA)>
++<!-- (AND|OR|NOT|RANGE|GROUP) --><!ELEMENT IdList (Id)*>
++<!ELEMENT Translation (From , To)>
++<!ELEMENT TranslationSet (Translation)*>
++<!ELEMENT TermSet (Term , Field , Count , Explode)>
++<!ELEMENT TranslationStack (TermSet | OP)*>
++<!-- Error message tags  --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT OutputMessage (#PCDATA)>
++<!-- .+ --><!ELEMENT QuotedPhraseNotFound (#PCDATA)>
++<!-- .+ --><!ELEMENT PhraseIgnored (#PCDATA)>
++<!-- .+ --><!ELEMENT FieldNotFound (#PCDATA)>
++<!-- .+ --><!ELEMENT PhraseNotFound (#PCDATA)>
++<!-- .+ --><!ELEMENT QueryTranslation (#PCDATA)>
++<!-- .+ --><!ELEMENT ErrorList (PhraseNotFound* , FieldNotFound*)>
++<!ELEMENT WarningList (PhraseIgnored* , QuotedPhraseNotFound* , OutputMessage*)>
++<!-- Response tags --><!ELEMENT eSearchResult (((Count , (RetMax , RetStart , QueryKey? , WebEnv? , IdList , TranslationSet , TranslationStack? , QueryTranslation)?) | ERROR) , ErrorList? , WarningList?)>
++]>
+ <eSearchResult>
+ 	<Count>534</Count>
+ 	<RetMax>20</RetMax>
+Index: libbio-eutilities-perl/t/data/eutils/esearch2.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/esearch2.xml
++++ libbio-eutilities-perl/t/data/eutils/esearch2.xml
+@@ -1,5 +1,36 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eSearchResult [
++<!--    
++                This is the Current DTD for Entrez eSearch
++$Id: eSearch_020511.dtd 85163 2006-06-28 17:35:21Z olegh $
++--><!-- ================================================================= --><!ELEMENT Count (#PCDATA)>
++<!-- \d+ --><!ELEMENT RetMax (#PCDATA)>
++<!-- \d+ --><!ELEMENT RetStart (#PCDATA)>
++<!-- \d+ --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ELEMENT From (#PCDATA)>
++<!-- .+ --><!ELEMENT To (#PCDATA)>
++<!-- .+ --><!ELEMENT Term (#PCDATA)>
++<!-- .+ --><!ELEMENT Field (#PCDATA)>
++<!-- .+ --><!ELEMENT QueryKey (#PCDATA)>
++<!-- \d+ --><!ELEMENT WebEnv (#PCDATA)>
++<!-- \S+ --><!ELEMENT Explode (#PCDATA)>
++<!-- (Y|N) --><!ELEMENT OP (#PCDATA)>
++<!-- (AND|OR|NOT|RANGE|GROUP) --><!ELEMENT IdList (Id)*>
++<!ELEMENT Translation (From , To)>
++<!ELEMENT TranslationSet (Translation)*>
++<!ELEMENT TermSet (Term , Field , Count , Explode)>
++<!ELEMENT TranslationStack (TermSet | OP)*>
++<!-- Error message tags  --><!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT OutputMessage (#PCDATA)>
++<!-- .+ --><!ELEMENT QuotedPhraseNotFound (#PCDATA)>
++<!-- .+ --><!ELEMENT PhraseIgnored (#PCDATA)>
++<!-- .+ --><!ELEMENT FieldNotFound (#PCDATA)>
++<!-- .+ --><!ELEMENT PhraseNotFound (#PCDATA)>
++<!-- .+ --><!ELEMENT QueryTranslation (#PCDATA)>
++<!-- .+ --><!ELEMENT ErrorList (PhraseNotFound* , FieldNotFound*)>
++<!ELEMENT WarningList (PhraseIgnored* , QuotedPhraseNotFound* , OutputMessage*)>
++<!-- Response tags --><!ELEMENT eSearchResult (((Count , (RetMax , RetStart , QueryKey? , WebEnv? , IdList , TranslationSet , TranslationStack? , QueryTranslation)?) | ERROR) , ErrorList? , WarningList?)>
++]>
+ <eSearchResult>
+ 	<Count>534</Count>
+ 	<RetMax>20</RetMax>
+Index: libbio-eutilities-perl/t/data/eutils/espell.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/espell.xml
++++ libbio-eutilities-perl/t/data/eutils/espell.xml
+@@ -1,5 +1,17 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eSpellResult PUBLIC "-//NLM//DTD eSpellResult, 23 November 2004//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSpell.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eSpellResult [
++<!--    
++This is the Current DTD for Entrez eSpell
++$Id:
++--><!-- ================================================================= --><!ELEMENT Original (#PCDATA)>
++<!-- \d+ --><!ELEMENT Replaced (#PCDATA)>
++<!-- \d+ --><!ELEMENT Database (#PCDATA)>
++<!-- \d+ --><!ELEMENT Query (#PCDATA)>
++<!-- \d+ --><!ELEMENT CorrectedQuery (#PCDATA)>
++<!-- \d+ --><!ELEMENT SpelledQuery (Replaced | Original)*>
++<!-- \d+ --><!ELEMENT ERROR (#PCDATA)>
++<!-- \d+ --><!ELEMENT eSpellResult (Database , Query , CorrectedQuery , SpelledQuery , ERROR)>
++]>
+ <eSpellResult>
+ 	<Database>pubmed</Database>
+ 	<Query>Netch AND Mus musclus</Query>
+Index: libbio-eutilities-perl/t/data/eutils/esummary1.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/esummary1.xml
++++ libbio-eutilities-perl/t/data/eutils/esummary1.xml
+@@ -1,5 +1,16 @@
+-<?xml version="1.0" encoding="ISO-8859-1"?>
+-<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult, 11 May 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd";>
++<?xml version="1.0" encoding="ISO-8859-1" standalone="yes"?>
++<!DOCTYPE eSummaryResult [
++<!--    
++This is the Current DTD for Entrez eSummary version 2
++$Id: eSummary_041029.dtd 49514 2004-10-29 15:52:04Z parantha $
++--><!-- ================================================================= --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ELEMENT Item (#PCDATA | Item)*>
++<!-- .+ --><!ATTLIST Item Name CDATA #REQUIRED>
++<!ATTLIST Item Type (Integer | Date | String | Structure | List | Flags | Qualifier | Enumerator | Unknown) #REQUIRED>
++<!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT DocSum (Id , Item+)>
++<!ELEMENT eSummaryResult (DocSum | ERROR)+>
++]>
+ <eSummaryResult>
+ 
+ <DocSum>
+Index: libbio-eutilities-perl/t/data/eutils/esummary2.xml
+===================================================================
+--- libbio-eutilities-perl.orig/t/data/eutils/esummary2.xml
++++ libbio-eutilities-perl/t/data/eutils/esummary2.xml
+@@ -1,5 +1,16 @@
+-<?xml version="1.0"?>
+-<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult, 29 October 2004//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd";>
++<?xml version="1.0" standalone="yes"?>
++<!DOCTYPE eSummaryResult [
++<!--    
++This is the Current DTD for Entrez eSummary version 2
++$Id: eSummary_041029.dtd 49514 2004-10-29 15:52:04Z parantha $
++--><!-- ================================================================= --><!ELEMENT Id (#PCDATA)>
++<!-- \d+ --><!ELEMENT Item (#PCDATA | Item)*>
++<!-- .+ --><!ATTLIST Item Name CDATA #REQUIRED>
++<!ATTLIST Item Type (Integer | Date | String | Structure | List | Flags | Qualifier | Enumerator | Unknown) #REQUIRED>
++<!ELEMENT ERROR (#PCDATA)>
++<!-- .+ --><!ELEMENT DocSum (Id , Item+)>
++<!ELEMENT eSummaryResult (DocSum | ERROR)+>
++]>
+ <eSummaryResult>
+ <DocSum>
+ 	<Id>32049</Id>
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..186087d
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+inline-DTDs-on-testsuite
-- 
2.11.0

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