From d077f0f686502ec00178d8fa0cb9c543b83fb67e Mon Sep 17 00:00:00 2001
From: jie zheng <jiezheng@upenn.edu>
Date: Fri, 25 Jan 2019 00:20:29 -0500
Subject: [PATCH] file for making release file

---
 Makefile | 159 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 159 insertions(+)
 create mode 100644 Makefile

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..c6cbebd
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,159 @@
+# OHMI ontology Makefile
+# Jie Zheng
+#
+# This Makefile is used to build artifacts
+# for the OHMI ontology.
+#
+
+### Configuration
+#
+# prologue:
+# <http://clarkgrubb.com/makefile-style-guide#toc2>
+
+MAKEFLAGS += --warn-undefined-variables
+SHELL := bash
+.SHELLFLAGS := -eu -o pipefail -c
+.DEFAULT_GOAL := all
+.DELETE_ON_ERROR:
+.SUFFIXES:
+
+### Definitions
+
+SHELL   := /bin/bash
+OBO     := http://purl.obolibrary.org/obo
+OHMI  := $(OBO)/OHMI_
+DEV     := $(OBO)/ohmi/dev
+TODAY   := $(shell date +%Y-%m-%d)
+
+### Directories
+#
+# This is a temporary place to put things.
+build:
+	mkdir -p $@
+
+
+### ROBOT
+#
+# We use the official development version of ROBOT
+# download the most recent build of ROBOT
+build/robot.jar: | build
+	@echo "Getting ROBOT" && \
+	curl -L -o $@ https://github.com/ontodev/robot/releases/download/v1.2.0/robot.jar
+
+ROBOT = java -jar build/robot.jar
+
+
+### Imports
+#
+# Use Ontofox to import various modules.
+#_build/import_%.owl: src/Ontofox-inputs/%_input.txt | build
+#_	curl -s -F file=@$< -o $@ http://ontofox.hegroup.org/service.php
+
+# Use ROBOT to ensure that serialization is consistent.
+#_src/ontology/Ontofox_outputs/%_import.owl: build/import_%.owl
+#_	$(ROBOT) convert -i build/$*_import.owl -o $@
+
+#_IMPORT_FILES := $(wildcard src/ontology/import/import_*.owl)
+
+#_.PHONY: imports
+#_imports: $(IMPORT_FILES)
+
+
+### Build
+#
+# Here we create a standalone OWL file appropriate for release.
+# This involves merging, reasoning, annotating,
+# and removing any remaining import declarations.
+build/ohmi_merged.owl: src/ontology/ohmi-edit.owl | build/robot.jar
+	@echo "Merging $< to $@" && \
+	$(ROBOT) merge \
+	--input $< \
+	annotate \
+	--ontology-iri "$(OBO)/ohmi/ohmi_merged.owl" \
+	--version-iri "$(OBO)/ohmi/$(TODAY)/ohmi_merged.owl" \
+	--annotation owl:versionInfo "$(TODAY)" \
+	--output build/ohmi_merged.tmp.owl
+	sed '/<owl:imports/d' build/ohmi_merged.tmp.owl > $@
+	rm build/ohmi_merged.tmp.owl
+
+ohmi.owl: build/ohmi_merged.owl | build/robot.jar
+	$(ROBOT) reason \
+	--input $< \
+	--reasoner HermiT \
+	annotate \
+	--ontology-iri "$(OBO)/ohmi.owl" \
+	--version-iri "$(OBO)/ohmi/$(TODAY)/ohmi.owl" \
+	--annotation owl:versionInfo "$(TODAY)" \
+	--output $@
+
+test_report.tsv: build/ohmi_merged.owl
+	$(ROBOT) report \
+	--input $< \
+        --fail-on none \
+	--output $@
+
+### Test
+#
+# Run main tests
+MERGED_VIOLATION_QUERIES := $(wildcard src/sparql/*-violation.rq)
+
+build/terms-report.csv: build/ohmi_merged.owl src/sparql/terms-report.rq | build
+	$(ROBOT) query --input $< --select $(word 2,$^) $@
+
+build/ohmi-previous-release.owl: | build
+	curl -L -o $@ "http://purl.obolibrary.org/obo/ohmi.owl"
+
+build/released-entities.tsv: build/ohmi-previous-release.owl src/sparql/get-ohmi-entities.rq | build/robot.jar
+	$(ROBOT) query --input $< --select $(word 2,$^) $@
+
+build/current-entities.tsv: build/ohmi_merged.owl src/sparql/get-ohmi-entities.rq | build/robot.jar
+	$(ROBOT) query --input $< --select $(word 2,$^) $@
+
+build/dropped-entities.tsv: build/released-entities.tsv build/current-entities.tsv
+	comm -23 $^ > $@
+
+# Run all validation queries and exit on error.
+.PHONY: verify
+verify: verify-merged verify-entities
+
+# Run validation queries on ohmi_merged and exit on error.
+.PHONY: verify-merged
+verify-merged: build/ohmi_merged.owl $(MERGED_VIOLATION_QUERIES) | build/robot.jar
+	$(ROBOT) verify --input $< --output-dir build \
+	--queries $(MERGED_VIOLATION_QUERIES)
+
+# Check if any entities have been dropped and exit on error.
+.PHONY: verify-entities
+verify-entities: build/dropped-entities.tsv
+	@echo $(shell < $< wc -l) " ohmi IRIs have been dropped"
+	@! test -s $<
+
+# Run a Hermit reasoner to find inconsistencies
+.PHONY: reason
+reason: build/ohmi_merged.owl | build/robot.jar
+	$(ROBOT) reason --input $< --reasoner HermiT
+
+.PHONY: test
+test: reason verify
+
+
+### General/Users/jiezheng/Documents/ontology/ohmi
+#
+# Full build
+.PHONY: all
+all: test ohmi.owl build/terms-report.csv
+
+# Remove generated files
+.PHONY: clean
+clean:
+	rm -rf build
+
+# Check for problems such as bad line-endings
+.PHONY: check
+check:
+	src/scripts/check-line-endings.sh tsv
+
+# Fix simple problems such as bad line-endings
+.PHONY: fix
+fix:
+	src/scripts/fix-eol-all.sh