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carandraug-guest pushed a commit to branch master
in repository libbio-eutilities-perl.
commit 1b786b48a502c89093b21c3e304fc0094463d68f
Author: Andreas Tille <ti...@debian.org>
Date: Fri Jan 27 13:00:02 2017 +0100
DEP3
---
debian/patches/inline-DTDs-on-testsuite | 155 ++++++++++++--------------------
1 file changed, 55 insertions(+), 100 deletions(-)
diff --git a/debian/patches/inline-DTDs-on-testsuite
b/debian/patches/inline-DTDs-on-testsuite
index 589c51c..8ce3ae1 100644
--- a/debian/patches/inline-DTDs-on-testsuite
+++ b/debian/patches/inline-DTDs-on-testsuite
@@ -1,7 +1,10 @@
-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
+Description: inline the DTDs in the xml files to prevent network access
+ when trying to build
+Author: Carnë Draug <carandraug+...@gmail.com>
+Last-Update: Thu, 26 Jan 2017 18:12:41 +0000
+
+--- a/t/data/eutils/egquery.xml
++++ b/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";>
@@ -28,10 +31,8 @@ Index: libbio-eutilities-perl/t/data/eutils/egquery.xml
<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
+--- a/t/data/eutils/einfo.xml
++++ b/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";>
@@ -70,10 +71,8 @@ Index: libbio-eutilities-perl/t/data/eutils/einfo.xml
<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
+--- a/t/data/eutils/einfo_dbs.xml
++++ b/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";>
@@ -112,10 +111,8 @@ Index: libbio-eutilities-perl/t/data/eutils/einfo_dbs.xml
<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
+--- a/t/data/eutils/elink_acheck.xml
++++ b/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";>
@@ -153,10 +150,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_acheck.xml
<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
+--- a/t/data/eutils/elink_acheck_corr.xml
++++ b/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";>
@@ -194,10 +189,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_acheck_corr.xml
<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
+--- a/t/data/eutils/elink_dball.xml
++++ b/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";>
@@ -235,10 +228,8 @@ Index: libbio-eutilities-perl/t/data/eutils/elink_dball.xml
<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
+--- a/t/data/eutils/elink_lcheck.xml
++++ b/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";>
@@ -276,10 +267,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_lcheck.xml
<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
+--- a/t/data/eutils/elink_lcheck_corr.xml
++++ b/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";>
@@ -317,10 +306,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_lcheck_corr.xml
<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
+--- a/t/data/eutils/elink_llinks.xml
++++ b/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";>
@@ -358,10 +345,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_llinks.xml
<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
+--- a/t/data/eutils/elink_llinks_corr.xml
++++ b/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";>
@@ -399,10 +384,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_llinks_corr.xml
<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
+--- a/t/data/eutils/elink_multidb.xml
++++ b/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";>
@@ -440,10 +423,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_multidb.xml
<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
+--- a/t/data/eutils/elink_multidb_corr.xml
++++ b/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";>
@@ -481,10 +462,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_multidb_corr.xml
<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
+--- a/t/data/eutils/elink_ncheck.xml
++++ b/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";>
@@ -522,10 +501,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_ncheck.xml
<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
+--- a/t/data/eutils/elink_ncheck_corr.xml
++++ b/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";>
@@ -563,10 +540,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_ncheck_corr.xml
<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
+--- a/t/data/eutils/elink_neighbor.xml
++++ b/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";>
@@ -604,10 +579,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_neighbor.xml
<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
+--- a/t/data/eutils/elink_neighbor_corr.xml
++++ b/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";>
@@ -645,10 +618,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_neighbor_corr.xml
<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
+--- a/t/data/eutils/elink_nhist.xml
++++ b/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";>
@@ -686,10 +657,8 @@ Index: libbio-eutilities-perl/t/data/eutils/elink_nhist.xml
<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
+--- a/t/data/eutils/elink_nhist_corr.xml
++++ b/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";>
@@ -727,10 +696,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_nhist_corr.xml
<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
+--- a/t/data/eutils/elink_scores.xml
++++ b/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";>
@@ -768,10 +735,8 @@ Index:
libbio-eutilities-perl/t/data/eutils/elink_scores.xml
<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
+--- a/t/data/eutils/epost.xml
++++ b/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";>
@@ -790,10 +755,8 @@ Index: libbio-eutilities-perl/t/data/eutils/epost.xml
<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
+--- a/t/data/eutils/esearch1.xml
++++ b/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";>
@@ -833,10 +796,8 @@ Index: libbio-eutilities-perl/t/data/eutils/esearch1.xml
<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
+--- a/t/data/eutils/esearch2.xml
++++ b/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";>
@@ -876,10 +837,8 @@ Index: libbio-eutilities-perl/t/data/eutils/esearch2.xml
<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
+--- a/t/data/eutils/espell.xml
++++ b/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";>
@@ -900,10 +859,8 @@ Index: libbio-eutilities-perl/t/data/eutils/espell.xml
<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
+--- a/t/data/eutils/esummary1.xml
++++ b/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";>
@@ -923,10 +880,8 @@ Index: libbio-eutilities-perl/t/data/eutils/esummary1.xml
<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
+--- a/t/data/eutils/esummary2.xml
++++ b/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";>
--
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