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Makefile
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TOP_DIR = ../..
include $(TOP_DIR)/tools/Makefile.common
TARGET ?= /kb/deployment
DEPLOY_RUNTIME ?= /kb/runtime
SERVER_SPEC = HomologyService.spec
#
# This layout is specfic to the current (January 2016) layout of
# the NCBI BLAST distribution.
#
BLAST_VERSION = 2.3.0
BLAST_BASE = ncbi-blast-$(BLAST_VERSION)+
BLAST_FTP_SRC = ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/$(BLAST_VERSION)/$(BLAST_BASE)-x64-linux.tar.gz
BLAST_FTP_FILE = $(notdir $(BLAST_FTP_SRC))
BLAST_DEPLOY_DIR = $(TARGET)/services/$(SERVICE)/bin
SERVICE_MODULE = lib/Bio/KBase/HomologyService/Service.pm
SERVICE = homology_service
SERVICE_NAME = HomologyService
SERVICE_PORT = 7134
#ASYNC_SERVICE_PORT = 7135
ASYNC_SERVICE_PSGI = HomologyServiceAsync.psgi
SERVICE_URL = https://kbase.us/services/$(SERVICE)
SERVICE_NAME = HomologyService
SERVICE_NAME_PY = $(SERVICE_NAME)
SERVICE_PSGI_FILE = $(SERVICE_NAME).psgi
SRC_SERVICE_PERL = $(wildcard service-scripts/*.pl)
BIN_SERVICE_PERL = $(addprefix $(BIN_DIR)/,$(basename $(notdir $(SRC_SERVICE_PERL))))
DEPLOY_SERVICE_PERL = $(addprefix $(SERVICE_DIR)/bin/,$(basename $(notdir $(SRC_SERVICE_PERL))))
ifdef TEMPDIR
TPAGE_TEMPDIR = --define kb_tempdir=$(TEMPDIR)
endif
TPAGE_ARGS = --define kb_top=$(TARGET) \
--define kb_runtime=$(DEPLOY_RUNTIME) \
--define kb_service=$(SERVICE) \
--define kb_service_name=$(SERVICE_NAME) \
--define kb_service_port=$(SERVICE_PORT) \
--define kb_psgi=$(SERVICE_PSGI_FILE) \
--define kb_async_service_port=$(ASYNC_SERVICE_PORT) \
--define kb_async_psgi=$(ASYNC_SERVICE_PSGI) \
$(TPAGE_TEMPDIR)
TESTS = $(wildcard t/client-tests/*.t)
all: bin compile-typespec service
test:
# run each test
echo "RUNTIME=$(DEPLOY_RUNTIME)\n"
for t in $(TESTS) ; do \
if [ -f $$t ] ; then \
$(DEPLOY_RUNTIME)/bin/perl $$t ; \
if [ $$? -ne 0 ] ; then \
exit 1 ; \
fi \
fi \
done
service:
compile-typespec: Makefile
mkdir -p lib/biop3/$(SERVICE_NAME_PY)
touch lib/biop3/__init__.py #do not include code in biop3/__init__.py
touch lib/biop3/$(SERVICE_NAME_PY)/__init__.py
mkdir -p lib/javascript/$(SERVICE_NAME)
compile_typespec \
--patric \
--psgi $(SERVICE_PSGI_FILE) \
--impl Bio::KBase::$(SERVICE_NAME)::%sImpl \
--service Bio::KBase::$(SERVICE_NAME)::Service \
--client Bio::KBase::$(SERVICE_NAME)::Client \
--py biop3/$(SERVICE_NAME_PY)/client \
--js javascript/$(SERVICE_NAME)/Client \
--url $(SERVICE_URL) \
--enable-retries \
$(SERVER_SPEC) lib
-rm -f lib/$(SERVER_MODULE)Server.py
-rm -f lib/$(SERVER_MODULE)Impl.py
-rm -f lib/CDMI_EntityAPIImpl.py
bin: $(BIN_PERL) $(BIN_SERVICE_PERL)
deploy: deploy-client deploy-service
deploy-all: deploy-client deploy-service
deploy-client: compile-typespec deploy-docs deploy-libs deploy-scripts
deploy-service: deploy-dir deploy-libs deploy-service-scripts deploy-blast
$(TPAGE) $(TPAGE_ARGS) service/start_service.tt > $(TARGET)/services/$(SERVICE)/start_service
chmod +x $(TARGET)/services/$(SERVICE)/start_service
$(TPAGE) $(TPAGE_ARGS) service/stop_service.tt > $(TARGET)/services/$(SERVICE)/stop_service
chmod +x $(TARGET)/services/$(SERVICE)/stop_service
deploy-service-scripts:
export KB_TOP=$(TARGET); \
export KB_RUNTIME=$(DEPLOY_RUNTIME); \
export KB_PERL_PATH=$(TARGET)/lib ; \
export PATH_PREFIX=$(TARGET)/services/$(SERVICE)/bin:$(TARGET)/services/cdmi_api/bin; \
for src in $(SRC_SERVICE_PERL) ; do \
basefile=`basename $$src`; \
base=`basename $$src .pl`; \
echo install $$src $$base ; \
cp $$src $(TARGET)/plbin ; \
$(WRAP_PERL_SCRIPT) "$(TARGET)/plbin/$$basefile" $(TARGET)/services/$(SERVICE)/bin/$$base ; \
done
deploy-blast: $(BLAST_DEPLOY_DIR)/blastp
$(BLAST_DEPLOY_DIR)/blastp:
if [ ! -s $(BLAST_FTP_FILE) ] ; then \
curl --fail -o $(BLAST_FTP_FILE) $(BLAST_FTP_SRC); \
fi
rm -rf blast.deploy
mkdir blast.deploy
tar -C blast.deploy -x -v -f $(BLAST_FTP_FILE)
mkdir -p $(BLAST_DEPLOY_DIR)
cp blast.deploy/$(BLAST_BASE)/bin/* $(BLAST_DEPLOY_DIR)
deploy-monit:
$(TPAGE) $(TPAGE_ARGS) service/process.$(SERVICE).tt > $(TARGET)/services/$(SERVICE)/process.$(SERVICE)
deploy-docs:
-mkdir doc
-mkdir $(SERVICE_DIR)
-mkdir $(SERVICE_DIR)/webroot
mkdir -p doc
$(DEPLOY_RUNTIME)/bin/pod2html -t "Homology Search Service API" lib/Bio/KBase/HomologyService/HomologyServiceImpl.pm > doc/homologyservice_impl.html
cp doc/*html $(SERVICE_DIR)/webroot/.
deploy-dir:
if [ ! -d $(SERVICE_DIR) ] ; then mkdir $(SERVICE_DIR) ; fi
if [ ! -d $(SERVICE_DIR)/webroot ] ; then mkdir $(SERVICE_DIR)/webroot ; fi
if [ ! -d $(SERVICE_DIR)/bin ] ; then mkdir $(SERVICE_DIR)/bin ; fi
$(BIN_DIR)/%: service-scripts/%.pl $(TOP_DIR)/user-env.sh
$(WRAP_PERL_SCRIPT) '$$KB_TOP/modules/$(CURRENT_DIR)/$<' $@
$(BIN_DIR)/%: service-scripts/%.py $(TOP_DIR)/user-env.sh
$(WRAP_PYTHON_SCRIPT) '$$KB_TOP/modules/$(CURRENT_DIR)/$<' $@
include $(TOP_DIR)/tools/Makefile.common.rules