include conf-Makefile
PELLET = java  -mx1024m -jar $(HOME)/src/pellet/lib/pellet.jar
SOURCE_DIR = ../../../ontology/OBO_REL
CURRENT_BFO_BRIDGE = 1-1
BFO_VERSIONS = 1-0 1-1
SRC = ro ro_bfo_bridge $(patsubst %,ro_bfo%_bridge,$(BFO_VERSIONS)) ro_full

FULL = \
  $(patsubst %,%.obo,$(SRC)) \
  $(patsubst %,%.owl,$(SRC)) \
  $(patsubst %,%.pro,$(SRC)) \
  $(patsubst %,%.obo-xml,$(SRC)) \
  $(patsubst %,%.obo.html,$(SRC)) \

RELEASE_FILES = $(FULL) 


all: $(FULL) check index.html
show: 
	echo $(FULL)

check: all_pellet all_obocheck

all_pellet:   $(patsubst %,%.pellet,$(SRC)) test_bfo.pellet
all_obocheck:   $(patsubst %,%.obocheck,$(SRC))

index.html: ro.html
	cp $< $@

clean:
	rm ro.obo-xml ro.obo index.html ro.html ro_bfo_bridge.obo ro_bfo_bridge.owl

# copy latest bridge to current file
ro_bfo_bridge.owl: ro_bfo$(CURRENT_BFO_BRIDGE)_bridge.owl
	cp ro_bfo$(CURRENT_BFO_BRIDGE)_bridge.owl $@

# version-specific BFO bridges - just change the header
ro_bfo%_bridge.obo:  $(SOURCE_DIR)/ro_bfo_bridge.obo
	cat $(SOURCE_DIR)/idspace-bfo$*.obo $(SOURCE_DIR)/ro_bfo_bridge.obo > $@.tmp && mv $@.tmp $@

# RO + Bridge : uses latest
ro_full.obo: ro.obo ro_bfo$(CURRENT_BFO_BRIDGE)_bridge.obo
	obo-merge-tags.pl -t idspace -t domain -t range -t relationship $< ro_bfo$(CURRENT_BFO_BRIDGE)_bridge.obo > $@.tmp && mv $@.tmp $@
.PRECIOUS: ro_full.obo

ro_full.owl: ro_full.obo
	echo 'import: http://www.ifomis.org/bfo/1.1' > import.obo && \
	cat import.obo $< > $<.plus_import.obo && \
	go2owl $<.plus_import.obo > $@.tmp && mv $@.tmp $@

# fetch from source
ro.obo: $(SOURCE_DIR)/ro_edit.obo
	cp $< $@
%.obo: $(SOURCE_DIR)/%.obo
	cp $< $@


# generic converters

#%.obo-xml: $(SOURCE_DIR)/%.obo relationship.xsl
#	go2obo_xml $< > $@.tmp && mv $@.tmp $@
%.obo-xml: %.obo
	go2obo_xml $< > $@.tmp && mv $@.tmp $@
.PRECIOUS: %.obo-xml

%.owl: %.obo
	go2owl $< > $@.tmp && mv $@.tmp $@
.PRECIOUS: %.owl

%.pellet: %.owl
	$(PELLET) -if $< > $@.tmp && mv $@.tmp $@

%.pro: %.obo-xml
	go2prolog $< > $@.tmp && mv $@.tmp $@

%.obo.html: %.obo
	obo-syntax-highlight-in-html.pl --title 'OBO Relation Ontology' $< > $@.tmp && mv $@.tmp $@

%.html: %.obo-xml relationship.xsl
	xsltproc ./relationship.xsl $< > $@.tmp && mv $@.tmp $@

%.roundtrip: %.obo
	obo2obo -allowdangling -o -allowdangling $@ $<
.PRECIOUS: %.roundtrip

# all except ro.obo will have dangling refs
ro.obocheck: ro.roundtrip
	obodiff ro.obo $< | grep -v OBO_REL:is_a > $@

%.obocheck: %.roundtrip
	touch $@

# prepare a release:
# creates a local subdirectory
# should only be executed once
prepare-%: all
	mkdir $* && \
	cp $(RELEASE_FILES) $* && \
	./mkdiff $*

# update main website - html only
update_site: all
	scp index.html $(WWW_DIR)

# update main website - html only
update_site2: all
	cp index.html ../ro
	cd ../ro && cvs commit -m '' index.html

# publishes a pre-release;
# ends up as http://obofoundry.org/ro/pre/<FILE>
# this directory is volatile
pub_prerelease: all
	scp $(RELEASE_FILES) $(WWW_DIR)/pre/

# publishes a release
# ends up as http://obofoundry.org/ro/N-NN/<FILE>
#        and http://obofoundry.org/ro/<FILE>
# involatile
# cvs tags release - ensures no duplicate releases
pub_release-%: all check %
	(cp ro.obo $(SOURCE_DIR)/ && cvs commit -m 'release' ro.obo && cd $(SOURCE_DIR) && cvs tag release-$* > TAG && grep -v NOT TAG) && \
	scp -r $* $(WWW_DIR)/
	scp -r $(RELEASE_FILES) $(WWW_DIR)/

# publishes a pre-release for a specific version;
# ends up as http://obofoundry.org/ro/pre/N-NN/<FILE>
# this directory is volatile
pub_prerelease-%: all check %/CHANGES
	scp -r $* $(WWW_DIR)/pre/