# ========================================
# Regulation XP test
# ========================================
# Anyone with oboedit2.29 or higher can generate these files
# Just change to this directory and type
#
#    make

#GO=../../ontology/gene_ontology_edit.obo
GO=../../ontology/editors/gene_ontology_write.obo
SOURCES= go_reglive_withPosNeg_withPF  go_reglive_withPosNeg_noPF go_reglive_noPosNeg_withPF  go_reglive_noPosNeg_noPF 
TARGETS= $(patsubst %,%.obo,$(SOURCES))

NU_RPT_UNFILTERED = new-terms-report-unfiltered.txt
RPT_UNFILTERED = report-unfiltered.txt
RPT_FILTERED = report-filtered.txt

# these two files are combined to make the full new set
NU = new-term-queue.obo new-terms-full.obo

all: $(TARGETS)  $(RPT_FILTERED) go_reglive_withPosNeg_withPF-newlinks.txt go_reglive_withPosNeg_withPF-abduced-links.txt go_reglive_withPosNeg_withPF-reasoned-filtered.obo go_reglive_withNew-reasoned-filtered.obo go_reglive_withPosNeg_withPF-bpgenus.obo
#all: $(TARGETS) go_reglive_withPosNeg_noPF-newlinks.txt go_reglive_withPosNeg_withPF-newlinks.txt

update:
	cd ../../ontology/editors && cvs update gene_ontology_write.obo

all_latest: update all

test: all $(patsubst %,%-test,$(TARGETS))
all_owl: all $(patsubst %,%.owl,$(SOURCES))
all_owlx: all $(patsubst %,%.owl-xml,$(SOURCES))

# ALL intersection_of tags present
# withPosNeg: Includes relationship: tags for regulates, positively_regulates and negatively_regulates
# withPF: Regulation of MF terms (in MP) have links to the corresponding terms (in MF)
go_reglive_withPosNeg_withPF.obo: $(GO)
	obo2obo -semanticparse -o $@ $< > $(RPT_UNFILTERED)
.PRECIOUS: go_reglive_withPosNeg_with_PF.obo

# run the reasoner over an .obo file and save both implied and asserted links
%-reasoned.obo: %.obo
	obo2obo -o -saveimpliedlinks $@ $< > $@.log  2>&1
.PRECIOUS: %-reasoned.obo

# run obol reasoner - oe reasoner seems to have some issues
%-newlinks.txt: %.obo
	blip-reasoner -i $< -explain genus_differentia > $@.tmp && mv $@.tmp $@

%-abduced-links.txt: %.obo
	blip -i $< -u query_go findall abduce_link/4 >  $@.tmp && mv $@.tmp $@

# ALL intersection_of tags present
# withPosNeg: Includes relationship: tags for regulates, positively_regulates and negatively_regulates
# noPF: Regulation of MF terms (in MP) DO NOT HAVE relationship tags to the corresponding terms (in MF)
#    (but the intersection_of tags do reference the MF term)
# *** this is the combination we will probably go with ***
%_withPosNeg_noPF.obo: %_withPosNeg_withPF.obo
	./obol-remove-inter-ontology-link.pl $< >  $@.tmp && mv $@.tmp $@
.PRECIOUS: %_withPosNeg_noPF.obo

# ALL intersection_of tags present
# noPosNeg: Includes relationship: tags for regulates, BUT NOT positively_regulates and negatively_regulates
# withPF: Regulation of MF terms (in MP) have links to the corresponding terms (in MF)
%_noPosNeg_withPF.obo: %_withPosNeg_withPF.obo
	egrep -v '^relationship: .*_regulates' $< > $@.tmp && mv $@.tmp $@
.PRECIOUS: %_noPosNeg_withPF.obo

# ALL intersection_of tags present
# noPosNeg: Includes relationship: tags for regulates, BUT NOT positively_regulates and negatively_regulates
# noPF: Regulation of MF terms (in MP) DO NOT HAVE relationship tags to the corresponding terms (in MF)
#    (but the intersection_of tags do reference the MF term)
%_noPosNeg_noPF.obo: %_noPosNeg_withPF.obo
	./obol-remove-inter-ontology-link.pl $< >  $@.tmp && mv $@.tmp $@
.PRECIOUS: %_noPosNeg_noPF.obo

%_noXP.obo: %.obo
	./obol-remove-or-replace-regulation-xps.pl $< > $@.tmp && mv $@.tmp $@

biological_process_xp_regulation.obo: go_reglive_withPosNeg_withPF.obo
	obo-grep.pl -r intersection_of $< | obo-filter-tags.pl -t id -t intersection_of > $@.tmp && mv $@.tmp $@


# this ontology includes terms in the term queue
%_withNew.obo: %_withPosNeg_noPF.obo $(NU)
	obo2obo -semanticparse -addsynonyms -o $@ $< $(NU) > $(NU_RPT_UNFILTERED)  2>&1
.PRECIOUS: %_withNew.obo

# experimental: new terms added here
new-term-queue.txt: $(GO)
	cvs update new-term-queue.txt
.PRECIOUS: new-term-queue.txt

new-term-queue.obo: new-term-queue.txt
	(./tq2obo.pl $< > $@.tmp) > $@.err && mv $@.tmp $@ 
#	grep regulation $< | (tbl2obo.pl > $@.tmp && mv $@.tmp $@) > $@.err  2>&1

%.owl: %.obo
	obo2owl -o file://`pwd`/$@ $<

%.owl-xml: %.obo
	obo2owl -owlformat owlxml -o file://`pwd`/$@ $<

# this is just an extra-paranoid test to see if the generated files can be parsed
%-test: %
	obo2obo -o $@.tmp $< && diff $@.tmp $< > $@ ; echo done

%-bpgenus.obo: %.obo
	perl -npe 's/intersection_of: GO:0065007.*/intersection_of: GO:0008150/' $< > $@.tmp && mv $@.tmp $@

%-filtered.obo: %.obo
	./filter.pl $< > $@
#	grep -v ^intersection_of: $< | egrep -v '^relationship:.*implied' > $@

$(RPT_FILTERED):  $(RPT_UNFILTERED)
	./filter-report.pl ../xps/biological_process_xp_self.obo ../xps/biological_process_xp_multi_organism_process.obo ../xps/biological_process_xp_cell.obo ../xps/biological_process_xp_uber_anatomy.obo regulates_QC_report_to_skip.txt $(RPT_UNFILTERED) | sort > $@

%-rx.obo: %.obo
	blip -i $< -debug rx -u go_transform_regulates io-convert -to obo -o $@