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commit e827f7d31448beddd8c326e5909199a8a0b2e403 Author: Carnë Draug <carandraug+...@gmail.com> Date: Thu Jan 26 18:01:49 2017 +0000 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(+) 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-perl/packages/libbio-eutilities-perl.git _______________________________________________ Pkg-perl-cvs-commits mailing list Pkg-perl-cvs-commits@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-perl-cvs-commits