rename update script

.gitignore

@@ -6,7 +6,7 @@ tools/symop-map-generator
 test/unit-test
 test/pdb2cif-test
 test/rename-compound-test
-tools/update-dictionary-script
+tools/update-libcifpp-data
 data/components.cif*
 CMakeSettings.json
 msvc/

CMakeLists.txt

@@ -287,16 +287,17 @@ if (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
     target_link_options(cifpp PRIVATE -undefined dynamic_lookup)
 endif (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
 
-# download the components.cif file from CCD
-set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif)
+option(DOWNLOAD_CCD "Download the CCD file components.cif during installation" OFF)
+if(DOWNLOAD_CCD)
+	# download the components.cif file from CCD
+	set(COMPONENTS_CIF ${PROJECT_SOURCE_DIR}/data/components.cif)
 
-if (NOT EXISTS ${COMPONENTS_CIF})
+	if (NOT EXISTS ${COMPONENTS_CIF})
 
 		if (NOT EXISTS ${PROJECT_SOURCE_DIR}/data)
 			file(MAKE_DIRECTORY ${PROJECT_SOURCE_DIR}/data/)
 		endif()
 
-	# if(${CMAKE_VERSION} VERSION_LESS "3.19.0")
 		find_program(GUNZIP gunzip)
 
 		if(GUNZIP)
@@ -309,16 +310,10 @@ if (NOT EXISTS ${COMPONENTS_CIF})
 			file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif ${COMPONENTS_CIF}
 				SHOW_PROGRESS)
 		endif()
-	# else()
-	# 	file(DOWNLOAD ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz ${COMPONENTS_CIF}.gz
-	# 		SHOW_PROGRESS)
-	# 	file(ARCHIVE_EXTRACT INPUT ${COMPONENTS_CIF}.gz
-	# 		DESTINATION ${CMAKE_SOURCE_DIR}/data/
-	# 		VERBOSE)
-	# endif()
-endif()
+	endif()
 
-add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
+	add_custom_target(COMPONENTS ALL DEPENDS ${COMPONENTS_CIF})
+endif()
 
 if(UNIX)
 	option(INSTALL_UPDATE_SCRIPT "Install the script to update CCD and dictionary files" OFF)
@@ -471,9 +466,9 @@ message("Will install in ${CMAKE_INSTALL_PREFIX}")
 if(INSTALL_UPDATE_SCRIPT)
 	set(CIFPP_CRON_DIR "$ENV{DESTDIR}/etc/cron.weekly")
 
-	configure_file(${CMAKE_SOURCE_DIR}/tools/update-dictionary-script.in update-dictionary-script @ONLY)
+	configure_file(${CMAKE_SOURCE_DIR}/tools/update-libcifpp-data.in update-libcifpp-data @ONLY)
 	install(
-		FILES ${CMAKE_CURRENT_BINARY_DIR}/update-dictionary-script
+		FILES ${CMAKE_CURRENT_BINARY_DIR}/update-libcifpp-data
 		DESTINATION ${CIFPP_CRON_DIR}
 		PERMISSIONS OWNER_EXECUTE OWNER_READ GROUP_EXECUTE GROUP_READ WORLD_EXECUTE WORLD_READ
 	)
@@ -482,13 +477,14 @@ if(INSTALL_UPDATE_SCRIPT)
 	install(DIRECTORY DESTINATION "$ENV{DESTDIR}/etc/libcifpp/cache-update.d")
 
 	# a config to, to make it complete
+	if(NOT EXISTS "$ENV{DESTDIR}/etc/libcifpp.conf")
 		file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf [[# Uncomment the next line to enable automatic updates
 # update=true
 ]])
 		install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libcifpp.conf DESTINATION "$ENV{DESTDIR}/etc")
+		install(CODE "message(\"A configuration file has been written to $ENV{DESTDIR}/etc/libcifpp.conf, please edit this file to enable automatic updates\")")
+	endif()
 
 	target_compile_definitions(cifpp PUBLIC CACHE_DIR="${CIFPP_CACHE_DIR}")
-
-	install(CODE "message(\"A configuration file has been written to $ENV{DESTDIR}/etc/libcifpp.conf, please edit this file to enable automatic updates\")")
 endif()
 

src/Compound.cpp

@@ -457,7 +457,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
 	{
 		ccd = cif::loadResource("components.cif");
 		if (not ccd)
-			throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-dictionary-script to fetch the data.");
+			throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data.");
 	}
 	else
 		ccd.reset(new std::ifstream(mCompoundsFile));
@@ -484,7 +484,7 @@ Compound *CCDCompoundFactoryImpl::create(const std::string &id)
 		{
 			ccd = cif::loadResource("components.cif");
 			if (not ccd)
-				throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-dictionary-script to fetch the data.");
+				throw std::runtime_error("Could not locate the CCD components.cif file, please make sure the software is installed properly and/or use the update-libcifpp-data to fetch the data.");
 		}
 		else
 			ccd.reset(new std::ifstream(mCompoundsFile));

tools/update-dictionary-script

+#!/bin/bash
+
+set -e
+
+if [ "$EUID" -ne 0 ]
+	then echo "Please run as root"
+	exit
+fi
+
+if [ -f /etc/libcifpp.conf ] ; then
+	. /etc/libcifpp.conf
+fi
+
+# check to see if we're supposed to run at all
+if [ "$update" != "true" ] ; then
+	exit
+fi
+
+# if cache directory doesn't exist, exit. 
+if ! [ -d /var/cache/libcifpp ]; then
+	exit
+fi
+
+fetch_dictionary () {
+	dict=$1
+	source=$2
+
+	wget -O${dict}.gz ${source}
+
+	# be careful not to nuke an existing dictionary file
+	# extract to a temporary file first
+
+	gunzip -c ${dict}.gz > ${dict}-tmp
+
+	# then move the extracted file to the final location
+
+	mv ${dict}-tmp ${dict}
+
+	# and clean up afterwards
+
+	rm ${dict}.gz
+}
+
+# fetch the dictionaries
+
+fetch_dictionary "/var/cache/libcifpp/mmcif_pdbx_v50.dic" "https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic.gz"
+fetch_dictionary "/var/cache/libcifpp/components.cif" "ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz"