DONT NOT MERGE (!) UPHENO: Installed ODK pipeline and first patterns

.gitignore

@@ -5,3 +5,17 @@ imports/*.tmp
 mp-edit.owl
 hp-edit.owl
 /obo-grep.pl
+src/old
+src/ontology/mirror
+src/ontology/mirror/*
+src/ontology/upheno.obo
+src/ontology/upheno.owl
+semantic.cache
+bin/
+src/ontology/seed.txt
+src/ontology/target/
+src/ontology/dosdp-tools.log
+src/patterns/imports/seed_sorted.txt
+src/ontology/ed_definitions_merged.owl
+src/ontology/patterns
+.DS_Store

src/metadata/README.md

@@ -0,0 +1,23 @@
+Metadata files for the OBO Library
+
+ * [upheno.yml](upheno.yml)
+     * Determines how your purl.obolibrary.org/obo/upheno/ redirects will be handled
+     * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config
+     * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config)
+     * Paste in the contents of [upheno.yml](upheno.yml)
+     * Click "Commit new file"
+     * IMPORTANT: remember to make a pull request
+     * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
+ * [upheno.md](upheno.md)
+     * Determines how your metadata is shown on OBO Library, OLS and AberOWL
+     * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology
+     * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology)
+     * Paste in the contents of [upheno.md](upheno.md)
+     * Click "Commit new file"
+     * IMPORTANT: remember to make a pull request
+     * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library*
+
+For more background see:
+
+ * http://obofoundry.org/
+ * http://obofoundry.org/faq/how-do-i-edit-metadata.html

src/metadata/upheno.md

@@ -0,0 +1,36 @@
+---
+layout: ontology_detail
+id: upheno
+title: upheno
+jobs:
+  - id: https://travis-ci.org/obophenotype/upheno
+    type: travis-ci
+build:
+  checkout: git clone https://github.com/obophenotype/upheno.git
+  system: git
+  path: "."
+contact:
+  email: [email protected]
+  label: Chris Mungall
+description: upheno is an ontology...
+domain: stuff
+homepage: https://github.com/obophenotype/upheno
+products:
+  - id: upheno.owl
+  - id: upheno.obo
+dependencies:
+ - id: iao
+ - id: go
+ - id: ro
+ - id: pato
+ - id: bfo
+ - id: chebi
+ - id: cl
+ - id: uberon
+tracker: https://github.com/obophenotype/upheno/issues
+license:
+  url: http://creativecommons.org/licenses/by/3.0/
+  label: CC-BY
+---
+
+Enter a detailed description of your ontology here

src/metadata/upheno.yml

@@ -0,0 +1,27 @@
+# PURL configuration for http://purl.obolibrary.org/obo/upheno
+
+idspace: UPHENO
+base_url: /obo/upheno
+
+products:
+- upheno.owl: https://raw.githubusercontent.com/obophenotype/upheno/master/upheno.owl
+- upheno.obo: https://raw.githubusercontent.com/obophenotype/upheno/master/upheno.obo
+
+term_browser: ontobee
+example_terms:
+- UPHENO_0000000
+
+entries:
+
+- prefix: /releases/
+  replacement: https://raw.githubusercontent.com/obophenotype/upheno/v
+
+- prefix: /tracker/
+  replacement: https://github.com/obophenotype/upheno/issues
+
+- prefix: /about/
+  replacement: http://www.ontobee.org/ontology/UPHENO?iri=http://purl.obolibrary.org/obo/
+
+## generic fall-through, serve direct from github by default
+- prefix: /
+  replacement: https://raw.githubusercontent.com/obophenotype/upheno/master/

src/ontology/Dockerfile

@@ -0,0 +1,3 @@
+FROM cmungall/osk
+
+CMD make test

src/ontology/Makefile

@@ -0,0 +1,237 @@
+# ----------------------------------------
+# Makefile for upheno
+# Generated using ontology-starter-kit
+# ----------------------------------------
+# <do not edit above this line>
+
+# ----------------------------------------
+# Standard Constants
+# ----------------------------------------
+# these can be overwritten on the command line
+
+OBO=http://purl.obolibrary.org/obo
+ONT=upheno
+BASE=$(OBO)/$(ONT)
+SRC=$(ONT)-edit.owl
+RELEASEDIR=../..
+ROBOT= robot
+OWLTOOLS= owltools
+USECAT= --use-catalog
+SPARQLDIR = ../sparql
+DOSDP_SCHEMA=http:// # change to PURL when ready.
+PATTERN_TESTER=simple_pattern_tester.py
+DOSDPT=dosdp-tools
+TARGET=target
+IMPORTS = iao go ro pato bfo chebi cl uberon
+
+
+# ----------------------------------------
+# Top-level targets
+# ----------------------------------------
+
+all: patterns all_imports sparql_test $(ONT).owl $(ONT).obo
+	echo 'Release files created successfully.'
+test: sparql_test all
+prepare_release: all
+	cp $(ONT).owl $(ONT).obo $(RELEASEDIR) &&\
+	mkdir -p $(RELEASEDIR)/imports &&\
+	cp imports/*.owl $(RELEASEDIR)/imports &&\
+	cp imports/*.obo $(RELEASEDIR)/imports &&\
+	git add $(RELEASEDIR)/imports/*.obo &&\
+	git add $(RELEASEDIR)/imports/*.owl &&\
+	(test -f subsets/*owl && cp subsets/* $(RELEASEDIR)/subsets && git add $(RELEASEDIR)/subsets/* || echo "no subsets") &&\
+	echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on github"
+
+# ----------------------------------------
+# Main release targets
+# ----------------------------------------
+
+# by default we use Elk to perform a reason-relax-reduce chain
+# after that we annotate the ontology with the release versionInfo
+$(ONT).owl: $(SRC)
+	$(ROBOT)  reason -i $< -r ELK -e none relax reduce -r ELK annotate -V $(BASE)/releases/`date +%Y-%m-%d`/$(ONT).owl -o $@ &&\
+	echo "$(ONT).owl successfully created."
+
+$(ONT).obo: $(ONT).owl
+	$(ROBOT) convert --check false -i $< -f obo -o $(ONT).obo.tmp && mv $(ONT).obo.tmp $@ &&\
+	echo "$(ONT).obo successfully created."
+
+# ----------------------------------------
+# Import modules
+# ----------------------------------------
+# Most ontologies are modularly constructed using portions of other ontologies
+# These live in the imports/ folder
+# These can be regenerated with make all_imports
+
+IMPORTS_OWL = $(patsubst %, imports/%_import.owl,$(IMPORTS)) $(patsubst %, imports/%_import.obo,$(IMPORTS)) $(patsubst %, imports/%_terms.txt,$(IMPORTS))
+
+# generate seed with all referenced entities
+
+ed_definitions_merged.owl: $(SRC) ../patterns/definitions.owl
+	$(ROBOT) merge -i $(SRC) -i ../patterns/definitions.owl -o $@
+
+seed.txt: ed_definitions_merged.owl
+	$(ROBOT) query -f csv -i $< --query ../sparql/terms.sparql $@
+
+# Generate terms.txt for each import.  # Assume OBO-style Possibly hacky step?
+# Should be able to drop this if robot can just take a big messy list of terms as input.
+
+imports/%_terms_combined.txt: seed.txt
+	cat $< imports/$*_terms.txt | sort | uniq >  $@
+
+# Make this target to regenerate ALL
+all_imports: $(IMPORTS_OWL)
+
+# Use ROBOT, driven entirely by terms lists NOT from source ontology
+imports/%_import.owl: mirror/%.owl imports/%_terms_combined.txt
+	$(ROBOT) extract -i $< -T imports/$*_terms_combined.txt --method BOT -O $(BASE)/$@ -o $@
+.PRECIOUS: imports/%_import.owl
+
+# convert imports to obo.
+# this can be useful for spot-checks and diffs.
+# we set strict mode to false by default. For discussion see https://github.com/owlcs/owlapi/issues/752
+imports/%_import.obo: imports/%_import.owl
+	$(ROBOT) convert --check false -i $< -f obo -o [email protected] && mv [email protected] $@
+
+# clone remote ontology locally, perfoming some excision of relations and annotations
+mirror/%.owl:
+	$(ROBOT) convert -I $(OBO)/$*.owl -o $@
+.PRECIOUS: mirror/%.owl
+
+# ----------------------------------------
+# Release
+# ----------------------------------------
+# copy from staging area (this directory) to top-level
+release: $(ONT).owl $(ONT).obo
+	cp $^ $(RELEASEDIR) && cp imports/* $(RELEASEDIR)/imports
+
+# ----------------------------------------
+# Sparql queries: Q/C
+# ----------------------------------------
+
+# these live in the ../sparql directory, and have suffix -violation.sparql
+# adding the name here will make the violation check live
+VCHECKS = equivalent-classes trailing-whitespace owldef-self-reference xref-syntax nolabels
+
+# Only needed until robot supports catalogs
+
+
+
+#  run all violation checks
+VQUERIES = $(foreach V,$(VCHECKS),$(SPARQLDIR)/$V-violation.sparql)
+sparql_test: $(SRC)
+	robot verify  --catalog catalog-v001.xml -i $< --queries $(VQUERIES) -O reports/
+
+# ----------------------------------------
+# Sparql queries: Reports
+ # ----------------------------------------
+
+REPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms
+REPORT_ARGS = $(foreach V,$(REPORTS),-s $(SPARQLDIR)/$V.sparql reports/$V.tsv)
+all_reports: $(SRC)
+	robot query -f tsv -i $< $(REPORT_ARGS)
+
+# ----------------------------------------
+# Docker (experimental)
+# ----------------------------------------
+IM=build-$(ONT)
+build-docker:
+	docker build -t $(ONT) .
+
+# ----------------------------------------
+# Patterns (experimental)
+# ----------------------------------------
+
+# Test patterns for schema compliance:
+
+
+# TODO - move declarations like this to top
+IMS=$(TARGET)/intermediates
+
+#PATTERN_IMPORTS = ../patterns/pattern.owl $(patsubst %, ../patterns/imports/%_import.owl,$(IMPORTS))
+
+
+# Better to make this an intermediate & merge with pattern.owl file having correct iri and import statements - configured by make
+
+
+# ----------------------------------------
+# Main command to generate the pattern ontology and the definitions
+# ----------------------------------------
+# The pattern.owl ontology contains the OWL versions of all the patterns currently in the patterns directory
+DOSDP_TEMP=$(IMS)/dosdp
+DOSDP_TEMP_PATTERN=$(DOSDP_TEMP)/patterns
+DOSDP_TEMP_PATTERN_MANUAL=$(DOSDP_TEMP_PATTERN)/manual
+DOSDP_TEMP_PATTERN_AUTO=$(DOSDP_TEMP_PATTERN)/auto
+DOSDP_TEMP_TERMS=$(DOSDP_TEMP)/terms
+DOSDP_TEMP_ONTOLOGIES=$(DOSDP_TEMP)/ontologies
+
+.PHONY patterns: ../patterns/pattern.owl ../patterns/definitions.owl
+
+pattern_clean:
+	rm -r $(DOSDP_TEMP)
+
+$(DOSDP_TEMP):
+	mkdir -p $@
+
+$(DOSDP_TEMP_PATTERN):
+	mkdir -p $@
+
+$(DOSDP_TEMP_TERMS):
+	mkdir -p $@
+
+$(DOSDP_TEMP_ONTOLOGIES):
+	mkdir -p $@
+
+$(DOSDP_TEMP_PATTERN_MANUAL): $(DOSDP_TEMP_PATTERN)
+	mkdir -p $@
+
+$(DOSDP_TEMP_PATTERN_AUTO): $(DOSDP_TEMP_PATTERN)
+	mkdir -p $@
+
+# ----------------------------------------
+# Build pattern.owl
+# ----------------------------------------
+# The pattern.owl ontology contains the OWL versions of all the patterns currently in the patterns directory
+
+../patterns/pattern.owl: pattern_schema_checks
+	$(DOSDPT) prototype --obo-prefixes --template=../patterns/dosdp-patterns --outfile=$@
+
+pattern_schema_checks:
+	simple_pattern_tester.py ../patterns/dosdp-patterns/ # 2>&1 | tee $@
+
+# ----------------------------------------
+# Build definitions.owl
+# ----------------------------------------
+# The following target will create a merged version of all imports indicated as project import dependencies (including the edit file itself), and then extract a module based
+# on the entities used in the TSV files
+individual_patterns_manual := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_MANUAL)/%.ofn, $(notdir $(wildcard ../patterns/data/manual/*.tsv)))
+individual_patterns_auto := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_AUTO)/%.ofn, $(notdir $(wildcard ../patterns/data/auto/*.tsv)))
+pattern_term_lists_auto := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_AUTO)/%.txt, $(notdir $(wildcard ../patterns/data/auto/*.tsv)))
+pattern_term_lists_manual := $(patsubst %.tsv, $(DOSDP_TEMP_PATTERN_MANUAL)/%.txt, $(notdir $(wildcard ../patterns/data/manual/*.tsv)))
+
+../patterns/definitions.owl: $(DOSDP_TEMP_PATTERN_MANUAL) $(individual_patterns_manual) $(individual_patterns_auto)
+	$(ROBOT) merge $(addprefix -i , $(individual_patterns_manual)) $(addprefix -i , $(individual_patterns_auto)) annotate --ontology-iri $(OBO)/$(ONT)/patterns/definitions.owl -o $@
+
+$(DOSDP_TEMP_PATTERN_MANUAL)/%.ofn: ../patterns/data/manual/%.tsv ../patterns/dosdp-patterns/%.yaml $(DOSDP_TEMP_ONTOLOGIES)/all_imports_module.owl $(DOSDP_TEMP_PATTERN_MANUAL)
+	dosdp-tools generate --infile=$< --template=$(word 2, $^) --ontology=$(word 3, $^) --obo-prefixes=true  --outfile=$@
+
+$(DOSDP_TEMP_PATTERN_AUTO)/%.ofn: ../patterns/data/auto/%.tsv ../patterns/dosdp-patterns/%.yaml $(DOSDP_TEMP_ONTOLOGIES)/all_imports_module.owl $(DOSDP_TEMP_PATTERN_AUTO)
+	dosdp-tools generate --infile=$< --template=$(word 2, $^) --ontology=$(word 3, $^) --obo-prefixes=true  --outfile=$@
+
+$(DOSDP_TEMP_ONTOLOGIES)/all_imports_module.owl: $(DOSDP_TEMP_ONTOLOGIES)/all_pattern_terms.txt $(DOSDP_TEMP_ONTOLOGIES)/all_imports.owl $(DOSDP_TEMP_ONTOLOGIES)
+	$(ROBOT) extract -i $(word 2, $^) -T $< --method BOT -o $@
+
+$(DOSDP_TEMP_ONTOLOGIES)/all_pattern_terms.txt: $(pattern_term_lists_auto) $(pattern_term_lists_manual) $(DOSDP_TEMP_ONTOLOGIES)
+	cat $^ $(word 2, $^) | sort | uniq >$@
+
+$(DOSDP_TEMP_PATTERN_MANUAL)/%.txt: ../patterns/dosdp-patterns/%.yaml ../patterns/data/manual/%.tsv $(DOSDP_TEMP_PATTERN_MANUAL)
+	dosdp-tools terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@
+
+$(DOSDP_TEMP_PATTERN_AUTO)/%.txt: ../patterns/dosdp-patterns/%.yaml ../patterns/data/auto/%.tsv $(DOSDP_TEMP_PATTERN_AUTO)
+	dosdp-tools terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@
+
+imports_all_pattern := $(patsubst %, mirror/%.owl,$(IMPORTS))
+
+$(DOSDP_TEMP_ONTOLOGIES)/all_imports.owl: $(imports_all_pattern)
+	echo 'imports: '$(imports_all_pattern) &&\
+	$(ROBOT) merge $(addprefix -i , $^) annotate --ontology-iri $(DOSDP_TEMP_ONTOLOGIES)/all_imports.owl -o $@