New port: science/opsin: Open Parser for Systematic IUPAC Nomenclatur…

…e of chemical names

science/Makefile

@@ -173,6 +173,7 @@
     SUBDIR += openmx
     SUBDIR += opensim-core
     SUBDIR += openstructure
+    SUBDIR += opsin
     SUBDIR += p5-Algorithm-SVMLight
     SUBDIR += p5-Chemistry-3DBuilder
     SUBDIR += p5-Chemistry-Bond-Find

science/opsin/Makefile

@@ -0,0 +1,62 @@
+# $FreeBSD$
+
+PORTNAME=	opsin
+DISTVERSION=	3.0.20190208
+CATEGORIES=	science java
+MASTER_SITES=	https://bitbucket.org/${BB_ACCOUNT}/${PORTNAME}/get/${BB_COMMIT}${EXTRACT_SUFX}?dummy=/:src
+DISTFILES=	${PORTNAME}-${DISTVERSION}${EXTRACT_SUFX}:src
+
+MAINTAINER=	[email protected]
+COMMENT=	Open Parser for Systematic IUPAC Nomenclature of chemical names
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+BUILD_DEPENDS=	mvn:devel/maven
+
+USE_JAVA=	yes
+
+NO_ARCH=	yes
+
+BB_ACCOUNT=	dan2097
+BB_COMMIT=	6688e0cedfcc
+
+WRKSRC=		${WRKDIR}/${BB_ACCOUNT}-${PORTNAME}-${BB_COMMIT}
+SUB_FILES=	${PORTNAME}
+SUB_LIST=	JAVA=${JAVA} PORTNAME=${PORTNAME} PORTVERSION=${PORTVERSION}
+
+PLIST_FILES=	bin/${PORTNAME} \
+		${JAVAJARDIR}/${PORTNAME}-${PORTVERSION}-jar-with-dependencies.jar
+
+# to rebuild the deps archive:
+#   1. set DEV_UPDATE_MODE=yes
+#   2. make makesum build
+#   3. upload the *-deps archive
+#   4. set DEV_UPDATE_MODE=no
+#   5. make clean makesum
+
+DEV_UPDATE_MODE=	no
+
+.if (${DEV_UPDATE_MODE} == "yes")
+post-build:
+	@cd ${WRKDIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} .m2
+	@${ECHO} "(!!!) Please upload the maven deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}"
+.else
+MASTER_SITES+=	LOCAL/yuri/:maven
+DISTFILES+=	${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:maven
+MVN_ARGS=	--offline
+.endif
+
+do-build:
+	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} \
+		${LOCALBASE}/bin/mvn ${MVN_ARGS} \
+		-fae install \
+		-Dmaven.test.skip=true \
+		-Duser.home=${WRKDIR} \
+		package assembly:assembly
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${WRKSRC}/target/${PORTNAME}-*-jar-with-dependencies.jar ${STAGEDIR}${JAVAJARDIR}/${PORTNAME}-${PORTVERSION}-jar-with-dependencies.jar
+
+.include <bsd.port.mk>

science/opsin/distinfo

@@ -0,0 +1,5 @@
+TIMESTAMP = 1550104217
+SHA256 (opsin-3.0.20190208.tar.gz) = d37222168a0ffb412109095212152f31b0b909abdaa14158561424651426df8f
+SIZE (opsin-3.0.20190208.tar.gz) = 1795278
+SHA256 (opsin-3.0.20190208-deps.tar.gz) = b42bfc011571d7e12fbc4e051653d19edaef6b7d04aaa146c817e1309dc4cba2
+SIZE (opsin-3.0.20190208-deps.tar.gz) = 20394666

science/opsin/files/opsin.in

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+export LC_ALL=en_US.UTF-8
+
+%%JAVA%% -jar %%JAVAJARDIR%%/%%PORTNAME%%-%%PORTVERSION%%-jar-with-dependencies.jar "$@"

science/opsin/pkg-descr

@@ -0,0 +1,6 @@
+OPSIN is a Java library for IUPAC name-to-structure conversion offering high
+recall and precision on organic chemical nomenclature.
+Supported outputs are SMILES, CML (Chemical Markup Language) and InChI (IUPAC
+International Chemical Identifier).
+
+WWW: https://bitbucket.org/dan2097/opsin/src/default/