biology/ncbi-entrez-direct: Update to 14.9.20210423_1

A few fixes to pass upstream test script

5 files changed, 17 insertions, 41 deletions

diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile
index 858e4734786c..7ece210acd5e 100644
--- a/biology/ncbi-entrez-direct/Makefile
+++ b/biology/ncbi-entrez-direct/Makefile
@@ -1,5 +1,6 @@
 PORTNAME=	ncbi-entrez-direct
 DISTVERSION=	14.9.20210423
+PORTREVISION=	1
 CATEGORIES=	biology perl5
 MASTER_SITES=	ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/${PORTVERSION}/
 DISTFILES=	edirect.tar.gz
@@ -13,7 +14,8 @@ LICENSE=	PD
 BUILD_DEPENDS=	bash:shells/bash
 RUN_DEPENDS=	p5-libwww>=0:www/p5-libwww \
 		p5-LWP-Protocol-https>=0:www/p5-LWP-Protocol-https \
-		p5-XML-Simple>=0:textproc/p5-XML-Simple
+		p5-XML-Simple>=0:textproc/p5-XML-Simple \
+		curl:ftp/curl
 
 USES=		go:modules perl5 shebangfix
 USE_GITHUB=	nodefault
@@ -22,7 +24,7 @@ USE_GITHUB=	nodefault
 #	make clean extract
 # 	cd ${WRKSRC}/cmd
 #	rm -r vendor
-#	../../../files/go-build
+#	../../../files/build-cmd
 # files/modules.txt: cd ${WRKSRC}/cmd && go mod vendor
 GHSD=		vendor/github.com
 GLSD=		vendor/golang.org
@@ -40,7 +42,7 @@ GH_TUPLE=	fatih:color:v1.10.0:a/${GHSD}/fatih/color \
 SHEBANG_FILES=	nquire edirect.pl word-at-a-time accn-at-a-time \
 		amino-acid-composition between-two-genes exclude-uid-lists \
 		filter-stop-words intersect-uid-lists phrase-search \
-		skip-if-file-exists theme-aliases
+		skip-if-file-exists theme-aliases test-edirect hgvs2spdi 
 
 PSCRIPTS=	efetch efilter einfo elink epost esearch esummary nquire
 SCRIPTS=	accn-at-a-time amino-acid-composition archive-pubmed \
@@ -54,7 +56,8 @@ SCRIPTS=	accn-at-a-time amino-acid-composition archive-pubmed \
 		reorder-columns run-ncbi-converter skip-if-file-exists \
 		ecommon.sh sort-uniq-count sort-uniq-count-rank stream-pubmed \
 		theme-aliases transmute word-at-a-time xml2tbl xtract xy-plot \
-		hlp-xtract.txt transmute xml2json xtract
+		hlp-xtract.txt transmute xml2json xtract test-edirect \
+		align-columns hgvs2spdi sort-table print-columns
 
 post-extract:
 	@${MV} ${WRKDIR}/edirect/* ${WRKSRC}
@@ -70,12 +73,11 @@ pre-configure:
 do-build:
 	@${CP} ${FILESDIR}/modules.txt ${WRKSRC}/cmd/vendor
 	@${CP} -R ${WRKSRC}/eutils ${WRKSRC}/cmd/vendor
-	@cd ${WRKSRC}/cmd && ${FILESDIR}/go-build
+	@cd ${WRKSRC}/cmd && ${FILESDIR}/build-cmd
 
 do-install:
 	cd ${WRKSRC} && ${INSTALL_SCRIPT} ${SCRIPTS} ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/edirect.pl ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_PROGRAM} ${WRKSRC}/cmd/*.FreeBSD ${STAGEDIR}${PREFIX}/bin
-	${INSTALL_SCRIPT} ${FILESDIR}/edirect-test.sh ${STAGEDIR}${PREFIX}/bin
 
 .include <bsd.port.mk>
diff --git a/biology/ncbi-entrez-direct/distinfo b/biology/ncbi-entrez-direct/distinfo
index be93ed84e5a1..e959f316b0e8 100644
--- a/biology/ncbi-entrez-direct/distinfo
+++ b/biology/ncbi-entrez-direct/distinfo
@@ -1,4 +1,4 @@
-TIMESTAMP = 1619301195
+TIMESTAMP = 1619443745
 SHA256 (edirect-14.9.20210423/edirect.tar.gz) = 9d6534226164fc5dfae7abcf25bfdbd08db068b27f1c13b8a3c4681cda5b0cea
 SIZE (edirect-14.9.20210423/edirect.tar.gz) = 829737
 SHA256 (edirect-14.9.20210423/fatih-color-v1.10.0_GH0.tar.gz) = a00342a7ffb8b119346dce56e152a111cbb9eab3970c429cc2ed4272aec2858e
diff --git a/biology/ncbi-entrez-direct/files/go-build b/biology/ncbi-entrez-direct/files/build-cmd
index d108b7da6209..1e2ad04bfde9 100755
--- a/biology/ncbi-entrez-direct/files/go-build
+++ b/biology/ncbi-entrez-direct/files/build-cmd
@@ -1,5 +1,8 @@
 #!/bin/sh -ex
 
+# This script replaces setup.sh, which is designed to download GO binaries
+# and dependencies and hence does not fit into a package manager build.
+
 platform=`uname -s`
 export HOME=$(pwd)
 go build -o xtract."$platform" xtract.go
diff --git a/biology/ncbi-entrez-direct/files/edirect-test.sh b/biology/ncbi-entrez-direct/files/edirect-test.sh
deleted file mode 100755
index 26da1db4ce88..000000000000
--- a/biology/ncbi-entrez-direct/files/edirect-test.sh
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/bin/sh -ex
-
-##########################################################################
-#   Function description:
-#       Pause until user presses return
-##########################################################################
-
-pause()
-{
-    local junk
-    
-    printf "Press return to continue..."
-    read junk
-}
-
-esearch -db pubmed -query "opsin gene conversion" | \
-  elink -related | \
-  elink -target protein
-pause
-
-esearch -db pubmed -query "lycopene cyclase" | efetch -format abstract
-pause
-
-esearch -db protein -query "lycopene cyclase" | efetch -format fasta
-pause
-
-esearch -db pubmed -query "opsin gene conversion" | \
-  elink -related | efilter -query "tetrachromacy"
-pause
-
-efilter -days 60 -datetype PDAT
-efilter -mindate 1990 -maxdate 1999 -datetype PDAT
-
diff --git a/biology/ncbi-entrez-direct/pkg-plist b/biology/ncbi-entrez-direct/pkg-plist
index 536ba728e03f..2ef17c29f959 100644
--- a/biology/ncbi-entrez-direct/pkg-plist
+++ b/biology/ncbi-entrez-direct/pkg-plist
@@ -1,4 +1,5 @@
 bin/accn-at-a-time
+bin/align-columns
 bin/amino-acid-composition
 bin/archive-pubmed
 bin/between-two-genes
@@ -6,7 +7,6 @@ bin/download-ncbi-data
 bin/download-pubmed
 bin/download-sequence
 bin/ecommon.sh
-bin/edirect-test.sh
 bin/edirect.pl
 bin/efetch
 bin/efilter
@@ -21,6 +21,7 @@ bin/expand-current
 bin/fetch-pubmed
 bin/filter-stop-words
 bin/gbf2xml
+bin/hgvs2spdi
 bin/hlp-xtract.txt
 bin/index-extras
 bin/index-pubmed
@@ -36,14 +37,17 @@ bin/pm-prepare
 bin/pm-promote
 bin/pm-refresh
 bin/pm-stash
+bin/print-columns
 bin/rchive
 bin/rchive.FreeBSD
 bin/reorder-columns
 bin/run-ncbi-converter
 bin/skip-if-file-exists
+bin/sort-table
 bin/sort-uniq-count
 bin/sort-uniq-count-rank
 bin/stream-pubmed
+bin/test-edirect
 bin/theme-aliases
 bin/transmute
 bin/transmute.FreeBSD