First pass at VALVE Validation

Makefile

@@ -56,7 +56,7 @@ templates = $(foreach i,$(build_files),--template $(i))
 
 ### Set Up
 
-build build/validate:
+build build/validate build/valve:
 	mkdir -p $@
 
 # We use the official development version of ROBOT for most things.
@@ -115,20 +115,35 @@ build/validation_errors.tsv: src/scripts/validate_templates.py index.tsv iedb/ie
 build/validation_errors_strict.tsv: src/scripts/validate_templates.py index.tsv iedb/iedb.tsv $(build_files)
 	python3 $< index.tsv iedb/iedb.tsv build $@
 
+VALVE_CONFIG := $(foreach f,$(shell ls src/validation),src/validation/$(f))
+
+$(VALVE_CONFIG): $(VALVE_CONFIG_MASTER) | build/valve
+	cp src/validation/* build/valve
+
+build/valve/%.tsv: ontology/%.tsv | build/valve
+	cp $< $@
+
+build/validation_valve.tsv: $(VALVE_CONFIG) $(source_files)
+	valve src/validation ontology -o $@ -r 3 || true
+
 apply_%: build/validation_%.tsv | .cogs
 	cogs clear all
 	cogs apply $<
 
 .PHONY: validate_tables
 validate_tables:
 	cogs fetch && cogs pull
+	cogs clear all
 	make apply_errors
+	make apply_valve
 	cogs push
 
 .PHONY: validate_tables_strict
 validate_tables_strict:
 	cogs fetch && cogs pull
+	cogs clear all
 	make apply_errors_strict
+	make apply_valve
 	cogs push
 
 ### Processing

ontology/core.tsv

@@ -1,7 +1,10 @@
 Label	IEDB Label	Class Type	Parent	Logic	Definition	Definition Source	Example of Usage
 LABEL	A OBI:9991118	CLASS_TYPE	C %	C %	A IAO:0000115	A IAO:0000119	A IAO:0000112
 Beta-2-microglobulin locus		subclass	genetic locus		The region of a chromosome that codes for Beta-2-microglobulin molecules.	IEDB	
-MHC haplotype		subclass	SO:0001024		A set of MHC alleles that is frequently inherited together.	IEDB	The mouse H-2-k class II haplotype is expressed in C3H mice.
+genetic locus		subclass	genetic entity				
+haplotype		subclass	genetic entity				
+haplotype_block		subclass	genetic entity				
+MHC haplotype		subclass	haplotype		A set of MHC alleles that is frequently inherited together.	IEDB	The mouse H-2-k class II haplotype is expressed in C3H mice.
 MHC ligand assay		subclass	immune epitope assay				
 MHC locus		subclass	genetic locus		The region of a chromosome that codes for MHC molecules.	IEDB	The class II regions encoding for the DP, DQ, and DR molecules on human chromosome 6.
 MHC protein complex with haplotype	haplotype	equivalent	MHC protein complex	('haplotype member of' some 'MHC haplotype')	A protein complex that is a member of an MHC haplotype.	IEDB	The mouse H-2-Kk molecule belongs to the H-2-k haplotype.

ontology/external.tsv

@@ -1,8 +1,12 @@
 ID	Label	Editor Preferred Term	IEDB Label	Class Type	Parent	Logic	Definition	Definition Source	Example of Usage	Source Ontology	Species Code
 ID	A rdfs:label	A IAO:0000111	A OBI:9991118	CLASS_TYPE	C %	C %	A IAO:0000115	A IAO:0000119	A IAO:0000112	AI IAO:0000412	
+BFO:0000040	material entity	material entity								http://purl.obolibrary.org/obo/bfo.owl
 ECO:0000000	evidence	evidence		subclass	information content entity					http://purl.obolibrary.org/obo/eco.owl	
+ECO:0000006	experimental evidence	experimental evidence		subclass	evidence					http://purl.obolibrary.org/obo/eco.owl
+ECO:0000033	author statement supported by traceable reference									http://purl.obolibrary.org/obo/eco.owl
 GO:0042611	MHC protein complex	MHC protein complex	MHC molecule	equivalent	protein complex	('has part' some (protein and ('gene product of' some 'MHC locus')))	A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.	GO		http://purl.obolibrary.org/obo/go.owl	
 GO:0043234	protein complex	protein complex	MHC	subclass	material entity					http://purl.obolibrary.org/obo/go.owl	
+IAO:0000030	information content entity	information content entity								http://purl.obolibrary.org/obo/iao.owl
 NCBITaxon:7959	grass carp	Ctenopharyngodon idella		subclass	organism					http://purl.obolibrary.org/obo/ncbitaxon.owl	Ctid
 NCBITaxon:8355	clawed frog	Xenopus laevis		subclass	organism					http://purl.obolibrary.org/obo/ncbitaxon.owl	Xela
 NCBITaxon:8839	duck	Anas platyrhynchos		subclass	organism					http://purl.obolibrary.org/obo/ncbitaxon.owl	Anpl
@@ -26,9 +30,12 @@ NCBITaxon:9940	sheep	Ovis aries		subclass	organism					http://purl.obolibrary.or
 NCBITaxon:9986	rabbit	Oryctolagus cuniculus		subclass	organism					http://purl.obolibrary.org/obo/ncbitaxon.owl	RLA
 NCBITaxon:10090	mouse	Mus musculus		subclass	organism					http://purl.obolibrary.org/obo/ncbitaxon.owl	H2
 NCBITaxon:10116	rat	Rattus norvegicus		subclass	organism					http://purl.obolibrary.org/obo/ncbitaxon.owl	RT1
+OBI:0100026	organism	organism		subclass	material entity					http://purl.obolibrary.org/obo/obi.owl
+OBI:1110128	immune epitope assay	immune epitope assay								http://purl.obolibrary.org/obo/obi.owl
+OBI:1110037	assay measuring binding of a T cell epitope:MHC:TCR complex	assay measuring binding of a T cell epitope:MHC:TCR complex		subclass	immune epitope assay					http://purl.obolibrary.org/obo/obi.owl
 PR:000000001	protein	protein		subclass	material entity					http://purl.obolibrary.org/obo/pr.owl	
 PR:000004580	Beta-2-microglobulin	Beta-2-microglobulin		equivalent	protein	('gene product of' some 'Beta-2-microglobulin locus')	A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof.			http://purl.obolibrary.org/obo/pr.owl	
-REO:0000079	genetic locus	genetic locus		subclass	genetic entity		a nucleic acid sequence region that is part of a genome and represents a specified location or region on a chromosome or other genomic element.			http://purl.obolibrary.org/obo/reo.owl	
-SO:0000355	haplotype_block	haplotype_block		subclass	genetic entity		A region of the genome which is co-inherited as the result of the lack of historic recombination within it.			http://purl.obolibrary.org/obo/so.owl	
-SO:0001024	haplotype	haplotype		subclass	genetic entity		A haplotype is one of a set of coexisting sequence variants of a haplotype block.			http://purl.obolibrary.org/obo/so.owl	
+REO:0000079	genetic locus	genetic locus					a nucleic acid sequence region that is part of a genome and represents a specified location or region on a chromosome or other genomic element.			http://purl.obolibrary.org/obo/reo.owl
+SO:0000355	haplotype_block	haplotype_block					A region of the genome which is co-inherited as the result of the lack of historic recombination within it.			http://purl.obolibrary.org/obo/so.owl
+SO:0001024	haplotype	haplotype					A haplotype is one of a set of coexisting sequence variants of a haplotype block.			http://purl.obolibrary.org/obo/so.owl
 owl:Thing	owl:Thing										

requirements.txt

@@ -1,4 +1,5 @@
 cerberus
 ontodev-cogs
 ontodev-gizmos==0.1.3
+ontodev-valve
 openpyxl

src/validation/datatype.tsv

@@ -0,0 +1,8 @@
+datatype	parent	match	level	description	instructions	replace
+blank		/^$/	ERROR	a blank value (an empty string)		
+line		/^[^\n]+$/	ERROR	a single line of text (no line breaks)	remove line breaks	s/\n/ /g
+trimmed line	line	/^\w.*\w$/	ERROR	a line with no leading or trailing whitespace	remove leading and trailing whitespace	s/\s+(.*)\s+/\1/
+label	trimmed line		ERROR	an ontology term label		
+IRI	trimmed line	/^\S+$/	ERROR	an Internationalized Resource Identifier	remove whitespace characters	
+prefix	trimmed line	/^\w+$/	ERROR	a valid prefix for a CURIE	remove non-word characters	
+numeric		/^[0-9]+$/	ERROR	a sequence of digits	remove non-numeric characters	

src/validation/field.tsv

@@ -0,0 +1,26 @@
+table	column	condition
+external	Parent	tree(Label)
+evidence	Conclusion	tree(Label, external.Parent)
+core	Parent	tree(Label, evidence.Conclusion)
+chain	Parent	tree(Label, core.Parent)
+genetic-locus	Parent	tree(Label, core.Parent)
+haplotype	Parent	tree(Label, core.Parent)
+molecule	Parent	tree(Label, core.Parent)
+mutant-molecule	Parent	tree(Label, core.Parent)
+serotype	Parent	tree(Label, core.Parent)
+chain	Parent	under(chain.Parent, "protein")
+external	ID	any(in("owl:Thing"), concat(in(prefix.prefix), ":", numeric))
+genetic-locus	Parent	under(genetic-locus.Parent, "genetic locus")
+haplotype-molecule	Parent	under(molecule.Parent, "protein complex")
+haplotype-molecule	In Taxon	under(external.Parent, "organism")
+haplotype-molecule	With Haplotype	under(haplotype.Parent, "haplotype")
+haplotype	Parent	under(haplotype.Parent, "haplotype")
+molecule	Parent	under(molecule.Parent, "protein complex")
+molecule	Alpha Chain	any(blank, in(chain.Label))
+molecule	Beta Chain	any(blank, in("Beta-2-microglobulin", chain.Label))
+molecule	With Haplotype	any(blank, under(haplotype.Parent, "haplotype"))
+molecule	With Serotype	any(blank, under(serotype.Parent, "serotype"))
+mutant-molecule	Parent	under(mutant-molecule.Parent, "mutant MHC protein complex")
+serotype-molecule	Parent	under(molecule.Parent, "protein complex")
+serotype-molecule	With Serotype	under(serotype.Parent, "serotype")
+serotype	Parent	under(serotype.Parent, "serotype")

src/validation/prefix.tsv

@@ -0,0 +1,14 @@
+prefix	base
+
+BFO	http://purl.obolibrary.org/obo/BFO_
+ECO	http://purl.obolibrary.org/obo/ECO_
+GO	http://purl.obolibrary.org/obo/GO_
+IAO	http://purl.obolibrary.org/obo/IAO_
+MRO	http://purl.obolibrary.org/obo/MRO_
+NCBITaxon	http://purl.obolibrary.org/obo/NCBITaxon_
+OBI	http://purl.obolibrary.org/obo/OBI_
+obo	http://purl.obolibrary.org/obo/
+owl	http://www.w3.org/2002/07/owl#
+PR	http://purl.obolibrary.org/obo/PR_
+REO	http://purl.obolibrary.org/obo/REO_
+SO	http://purl.obolibrary.org/obo/SO_

src/validation/rule.tsv

@@ -0,0 +1,9 @@
+table	when column	when condition	then column	then condition	level	description
+chain	Parent	in("protein")	Gene	under(genetic-locus.Parent, "genetic locus")	ERROR	
+external	Label	not(in("owl:Thing"))	Source Ontology	not(blank)	ERROR	
+genetic-locus	Parent	under(genetic-locus.Parent, "MHC locus", direct=True)	In Taxon	under(external.Parent, "organism")	ERROR	
+haplotype	Parent	in("MHC haplotype")	In Taxon	under(external.Parent, "organism")	ERROR	
+molecule	Parent	not(in("MHC protein complex"))	In Taxon	under(external.Parent, "organism")	ERROR	
+mutant-molecule	Parent	under(mutant-molecule.Parent, "mutant MHC protein complex", direct=True)	In Taxon	under(external.Parent, "organism")	ERROR	
+mutant-molecule	Parent	not(any(in("mutant MHC protein complex"), under(mutant-molecule.Parent, "mutant MHC protein complex", direct=True)))	Mutant Of	under(molecule.Parent, "protein complex")	ERROR	
+serotype-molecule	Parent	not(any(in("MHC protein complex"), under(serotype.Parent, "MHC serotype", direct=True)))	In Taxon	under(external.Parent, "organism")	ERROR