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_dynamic_files.jinja2
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{#-
Jinja2 Template for multile dynamic files
See odk.py for how this is processed.
This is first expanded into a single text file;
Each entry starting with ^^^ denotes a single file
-#}
{#-
Ontology source file, e.g. src/ontology/foo-edit.owl
We seed this with basic info such as ontology IRI and
a fake root class (this can be customized).
Note that when running odk.py, you can pass in a --source
argument to substitute this with your own edit file
#}
^^^ src/ontology/{{ project.id }}-edit.{{ project.edit_format }}
{% if project.edit_format == "obo" %}
format-version: 1.2
{% if project.import_group is defined -%}
{% if project.import_group.use_base_merging %}
import: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/merged_import.owl
{% else %}
{% for imp in project.import_group.products %}
import: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/{{ imp.id }}_import.owl
{% endfor %}
{% endif %}
{% endif %}
{%- if project.use_dosdps %}
import: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/patterns/definitions.owl
{%- if project.import_pattern_ontology %}
import: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/patterns/pattern.owl
{% endif -%}
{% endif %}
ontology: {{project.id}}
property_value: http://purl.org/dc/terms/description "{{ project.description }}" xsd:string
property_value: http://purl.org/dc/terms/title "{{ project.title }}" xsd:string
property_value: http://purl.org/dc/terms/license {{ project.license }}
[Term]
id: {{ project.id | upper }}:0000000
name: root node
[Typedef]
id: http://purl.org/dc/terms/description
name: description
is_metadata_tag: true
[Typedef]
id: http://purl.org/dc/terms/title
name: title
is_metadata_tag: true
[Typedef]
id: http://purl.org/dc/terms/license
name: license
is_metadata_tag: true
{% else %}
Prefix(:=<{{ project.uribase }}/{{ project.id }}.owl#>)
Prefix(dce:=<http://purl.org/dc/elements/1.1/>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(dcterms:=<http://purl.org/dc/terms/>)
Ontology(<{{ project.uribase }}/{{ project.id }}.owl>
{% if project.import_group is defined -%}
{% if project.import_group.use_base_merging %}
Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/merged_import.owl>)
{% else %}
{% for imp in project.import_group.products %}
Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/{{ imp.id }}_import.owl>)
{% endfor %}
{% endif %}
{% endif %}
{%- if project.use_dosdps %}
Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/patterns/definitions.owl>)
{%- if project.import_pattern_ontology %}
Import(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/patterns/pattern.owl>)
{% endif -%}
{% endif %}
Annotation(dcterms:description "{{ project.description }}")
Annotation(dcterms:license <{{ project.license }}>)
Annotation(dcterms:title "{{ project.title }}")
Declaration(Class(<{{ project.uribase }}/{{ project.id | upper }}_0000000>))
Declaration(AnnotationProperty(dcterms:description))
Declaration(AnnotationProperty(dcterms:license))
Declaration(AnnotationProperty(dcterms:title))
############################
# Annotation Properties
############################
AnnotationAssertion(rdfs:label dcterms:description "description")
AnnotationAssertion(rdfs:label dcterms:license "license")
AnnotationAssertion(rdfs:label dcterms:title "title")
############################
# Classes
############################
# Class: <{{ project.uribase }}/{{ project.id | upper }}_0000000> (root node)
AnnotationAssertion(rdfs:label <{{ project.uribase }}/{{ project.id | upper }}_0000000> "root node"@en)
)
{% endif %}
{#-
ID ranges file
#}
^^^ src/ontology/{{ project.id }}-idranges.owl
## ID Ranges File
Prefix: rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
Prefix: idsfor: <http://purl.obolibrary.org/obo/IAO_0000598>
Prefix: dce: <http://purl.org/dc/elements/1.1/>
Prefix: xsd: <http://www.w3.org/2001/XMLSchema#>
Prefix: allocatedto: <http://purl.obolibrary.org/obo/IAO_0000597>
Prefix: xml: <http://www.w3.org/XML/1998/namespace>
Prefix: idprefix: <http://purl.obolibrary.org/obo/IAO_0000599>
Prefix: iddigits: <http://purl.obolibrary.org/obo/IAO_0000596>
Prefix: rdfs: <http://www.w3.org/2000/01/rdf-schema#>
Prefix: idrange: <http://purl.obolibrary.org/obo/ro/idrange/>
Prefix: owl: <http://www.w3.org/2002/07/owl#>
Ontology: <{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/{{ project.id }}-idranges.owl>
Annotations:
idsfor: "{{ project.id | upper }}",
idprefix: "{{ project.uribase }}/{{ project.id | upper }}_",
iddigits: 7
AnnotationProperty: idprefix:
AnnotationProperty: iddigits:
AnnotationProperty: idsfor:
AnnotationProperty: allocatedto:
Datatype: idrange:1
Annotations:
allocatedto: "ONTOLOGY-CREATOR"
EquivalentTo:
xsd:integer[>= 0 , <= 999999]
Datatype: idrange:2
Annotations:
allocatedto: "ADDITIONAL EDITOR"
EquivalentTo:
xsd:integer[>= 1000000 , <= 1999999]
Datatype: xsd:integer
Datatype: rdf:PlainLiteral
^^^ src/ontology/{{ project.id }}.Makefile
## Customize Makefile settings for {{project.id}}
##
## If you need to customize your Makefile, make
## changes here rather than in the main Makefile
{% if project.import_group is defined -%}
{%- if 'custom' == project.import_group.module_type %}
imports/%_import.owl: mirror/%.owl
echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in {{ project.id }}.Makefile!" && touch $@
{% endif %}
{%- endif %}
{% if project.import_group.use_base_merging %}
{#-
Single merged import file
#}
^^^ src/ontology/imports/merged_import.owl
Prefix(:=<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/merged_import.owl>)
Prefix(obo:=<http://purl.obolibrary.org/obo/>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
Ontology(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/merged_import.owl>
# This is a placeholder, it will be regenerated when makefile is first executed.
)
{% else %}
{#-
Imports files, one per import
#}
{% for imp in project.import_group.products %}
^^^ src/ontology/imports/{{ imp.id }}_import.owl
Prefix(:=<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/{{ imp.id }}_import.owl>)
Prefix(obo:=<http://purl.obolibrary.org/obo/>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
Ontology(<{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/imports/{{ imp.id }}_import.owl>
# This is a placeholder, it will be regenerated when makefile is first executed.
)
{% endfor %}
{% endif %}
{#-
Import Term files
We seed each of these with some random terms. This is a little unsatisfactory and fragile;
ROBOT extract will fail if it cannot find any of the terms. While this doesn't matter in the long term,
as the ontology maintainer will provide their own lists, but it is problematic for the initial seed.
TODO: Decide if we should either query ontobee for seed terms OR have the seed list provided in the project.yaml
#}
{% for imp in project.import_group.products %}
^^^ src/ontology/imports/{{ imp.id }}_terms.txt
{% endfor %}
{#-
Metadata files.
These are convenient for submission to OBO. Note that OBO maintains two files, a .md and a .yml
TODO: include a script that makes it easy for maintainers to do this.
#}
{%- if project.create_obo_metadata %}
^^^ src/metadata/README.md
Metadata files for the OBO Library
* [{{ project.id }}.yml]({{ project.id }}.yml)
* Determines how your purl.obolibrary.org/obo/{{ project.id }}/ 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 [{{ project.id }}.yml]({{ project.id }}.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*
* [{{ project.id }}.md]({{ project.id }}.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 [{{ project.id }}.md]({{ project.id }}.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/{{ project.id }}.md
---
layout: ontology_detail
id: {{ project.id }}
title: {{ project.title }}
jobs:
- id: https://travis-ci.org/{{ project.github_org }}/{{ project.repo }}
type: travis-ci
build:
checkout: git clone https://github.com/{{ project.github_org }}/{{ project.repo }}.git
system: git
path: "."
contact:
email: {{ project.contact.email }}
label: {{ project.contact.name }}
github: {{ project.contact.github }}
description: {{ project.title }} is an ontology...
domain: stuff
homepage: https://github.com/{{ project.github_org }}/{{ project.repo }}
products:
- id: {{ project.id }}.owl
name: "{{ project.title }} main release in OWL format"
- id: {{ project.id }}.obo
name: "{{ project.title }} additional release in OBO format"
- id: {{ project.id }}.json
name: "{{ project.title }} additional release in OBOJSon format"
- id: {{ project.id }}/{{ project.id }}-base.owl
name: "{{ project.title }} main release in OWL format"
- id: {{ project.id }}/{{ project.id }}-base.obo
name: "{{ project.title }} additional release in OBO format"
- id: {{ project.id }}/{{ project.id }}-base.json
name: "{{ project.title }} additional release in OBOJSon format"
dependencies:
{% for imp in project.import_group.products -%}
- id: {{ imp.id }}
{% endfor %}
tracker: https://github.com/{{ project.github_org }}/{{ project.repo }}/issues
license:
url: http://creativecommons.org/licenses/by/3.0/
label: CC-BY
activity_status: active
---
Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML.
You can also embed images too.
^^^ src/metadata/{{ project.id }}.yml
# PURL configuration for http://purl.obolibrary.org/obo/{{ project.id }}
idspace: {{ project.id|upper }}
base_url: /obo/{{ project.id }}
products:
- {{ project.id }}.owl: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/{{ project.git_main_branch }}/{{ project.id }}.owl
- {{ project.id }}.obo: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/{{ project.git_main_branch }}/{{ project.id }}.obo
term_browser: ontobee
example_terms:
- {{ project.id.upper() }}_0000000
entries:
- prefix: /releases/
replacement: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/v
- prefix: /tracker/
replacement: https://github.com/{{ project.github_org }}/{{ project.repo }}/issues
- prefix: /about/
replacement: http://www.ontobee.org/ontology/{{ project.id|upper }}?iri=http://purl.obolibrary.org/obo/
## generic fall-through, serve direct from github by default
- prefix: /
replacement: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/{{ project.git_main_branch }}/
{%- endif %}
{% if project.use_templates %}
^^^ src/templates/README.md
# ROBOT templates
{%- if project.components is not none %}
{%- for component in project.components.products %}
{%- if component.use_template %}
{%- if component.templates is not none %}{% for template in component.templates %}
^^^ src/templates/{{ template }}
ID LABEL
ID LABEL
{%- endfor %}{% else %}
^^^ src/templates/{{ component.filename.split('.') | first }}.tsv
ID LABEL
ID LABEL
{%- endif %}
{%- endif %}
{%- endfor %}
{%- endif %}
{%- endif %}
{%- if project.use_mappings %}
^^^ src/mappings/README.md
# Directory for managing SSSOM mappings files
{%- if project.sssom_mappingset_group is not none %}
{%- for mapping in project.sssom_mappingset_group.products %}
^^^ src/mappings/{{ mapping.id }}.sssom.tsv
# curie_map:
# semapv: https://w3id.org/semapv/
# skos: http://www.w3.org/2004/02/skos/core#
# sssom: https://w3id.org/sssom/
# {{ project.id | upper }}: {{ project.uribase }}/{{ project.id | upper }}_
# license: https://creativecommons.org/publicdomain/zero/1.0/
# mapping_set_id: http://purl.obolibrary.org/obo/{{ project.id }}/mappings/{{ mapping.id }}.sssom.tsv
subject_id predicate_id object_id mapping_justification
{{ project.id | upper }}:0000000 skos:exactMatch sssom:NoTermFound semapv:ManualMappingCuration
{%- endfor %}
{%- endif %}
{%- endif %}
{%- if project.use_translations %}
^^^ src/translations/README.md
# Directory for managing translation files
{%- if project.babelon_translation_group is not none %}
{%- for translation in project.babelon_translation_group.products %}
^^^ src/translations/{{ translation.id }}.babelon.tsv
source_language translation_language subject_id predicate_id source_value translation_value translation_status
{%- if translation.include_robot_template_synonyms %}
^^^ src/translations/{{ translation.id }}.synonyms.tsv
subject_id translation_value comment
ID AL oboInOwl:hasExactSynonym@{{ translation.language }}
{%- endif %}
{%- endfor %}
{%- endif %}
{%- endif %}
{#-
Example pattern implementation TSV
#}
{%- if project.use_dosdps %}
^^^ src/patterns/definitions.owl
Prefix(:=<http://purl.obolibary.org/obo/{{ project.id }}/definitions.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Ontology(<http://purl.obolibary.org/obo/{{ project.id }}/definitions.owl>
)
^^^ src/patterns/pattern.owl
Prefix(:=<http://purl.obolibary.org/obo/{{ project.id }}/pattern.owl#>)
Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
Ontology(<http://purl.obolibary.org/obo/{{ project.id }}/pattern.owl>
)
^^^ src/patterns/README.md
# DOSDP patterns - editors docs
^^^ src/patterns/data/default/example.tsv
defined_class example
^^^ src/patterns/dosdp-patterns/example.yaml
pattern_name: example
pattern_iri: {{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/example.yaml
description: "This is a minimal example pattern."
classes:
example: owl:Thing
relations:
part_of: BFO:0000050
vars:
example: "'example'"
name:
text: "Part of %s"
vars:
- example
equivalentTo:
text: "'part_of' some %s"
vars:
- example
^^^ src/patterns/dosdp-patterns/external.txt
^^^ src/patterns/data/default/README.md
Documentation of the Default DOSDP Pipeline
{%- if project.pattern_pipelines_group is defined %}
{%- for pipeline in project.pattern_pipelines_group.products %}
^^^ src/patterns/data/{{ pipeline.id }}/README.md
# Documentation of the {{ pipeline.id }} DOSDP Pipeline
{%- endfor %}
{%- endif %}
{%- endif %}
{%- if project.use_context %}
^^^ src/ontology/config/context.json
{
"@context": {
"obo": "http://purl.obolibrary.org/obo/",
"oboInOwl": "http://www.geneontology.org/formats/oboInOwl#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"rdfa": "http://www.w3.org/ns/rdfa#",
"xml": "http://www.w3.org/XML/1998/namespace",
"xsd": "http://www.w3.org/2001/XMLSchema#",
"owl": "http://www.w3.org/2002/07/owl#",
"dc": "http://purl.org/dc/terms/",
"foaf": "http://xmlns.com/foaf/0.1/",
"prov": "http://www.w3.org/ns/prov#",
"skos": "http://www.w3.org/2004/02/skos/core#",
"void": "http://rdfs.org/ns/void#"
}
}
{%- endif %}
{#-
SPARQL QUERY to collect all terms that belong to an ontology
#}
^^^ src/sparql/{{ project.id }}_terms.sparql
SELECT DISTINCT ?term
WHERE {
{ ?s1 ?p1 ?term . }
UNION
{ ?term ?p2 ?o2 . }
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
}
{#-
SPARQL QUERY QC checks
#}
{%- if project.robot_report.custom_sparql_checks is not defined or 'owldef-self-reference' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/owldef-self-reference-violation.sparql
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?term WHERE {
{ ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] }
UNION
{ ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] }
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'redundant-subClassOf' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/redundant-subClassOf-violation.sparql
PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?term ?xl ?y ?yl ?z ?zl WHERE {
?term rdfs:subClassOf ?y ;
rdfs:label ?xl .
?y rdfs:subClassOf+ ?z ;
rdfs:label ?yl .
?term rdfs:subClassOf ?z .
?z rdfs:label ?zl .
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'taxon-range' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/taxon-range-violation.sparql
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
SELECT ?term ?property ?taxon
WHERE {
VALUES ?property { never_in_taxon: present_in_taxon: }
?term ?property ?taxon .
FILTER (!isIRI(?taxon) || !STRSTARTS(STR(?taxon), "http://purl.obolibrary.org/obo/NCBITaxon_"))
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'iri-range' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/iri-range-violation.sparql
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?term ?property ?value
WHERE {
VALUES ?property {
never_in_taxon:
present_in_taxon:
foaf:depicted_by
oboInOwl:inSubset
dcterms:contributor }
?term ?property ?value .
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
FILTER (!isIRI(?value))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'iri-range-advanced' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/iri-range-advanced-violation.sparql
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
SELECT ?term ?property ?value
WHERE {
VALUES ?property {
never_in_taxon:
present_in_taxon:
rdfs:seeAlso
foaf:depicted_by
oboInOwl:inSubset
dcterms:contributor }
?term ?property ?value .
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
FILTER (!isIRI(?value))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'label-with-iri' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/label-with-iri-violation.sparql
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?term ?value
WHERE {
?term rdfs:label ?value .
FILTER (REGEX(?value, "http[s]?[:]"))
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'multiple-replaced_by' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/multiple-replaced_by-violation.sparql
PREFIX replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
SELECT DISTINCT ?entity ?property ?value WHERE {
VALUES ?property {
replaced_by:
}
?entity ?property ?value1 .
?entity ?property ?value2 .
FILTER(?value1!=?value2)
BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value)
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'term-tracker-uri' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/term-tracker-uri-violation.sparql
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX term_tracker_item: <http://purl.obolibrary.org/obo/IAO_0000233>
SELECT ?term ?term_tracker ?term_tracker_type WHERE {
?term term_tracker_item: ?term_tracker .
FILTER(DATATYPE(?term_tracker) != xsd:anyURI)
BIND(DATATYPE(?term_tracker) as ?term_tracker_type)
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'illegal-date' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/illegal-date-violation.sparql
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
SELECT DISTINCT ?term ?property ?value WHERE
{
VALUES ?property {dct:date dct:issued dct:created oboInOwl:creation_date}
?term ?property ?value .
FILTER (datatype(?value) != xsd:date || !regex(str(?value), '^\\d{4}-\\d\\d-\\d\\d$'))
FILTER (datatype(?value) != xsd:dateTime || !regex(str(?value), '^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z'))
}
{% endif %}
{%- if project.robot_report.custom_sparql_checks is not defined or 'dc-properties' in project.robot_report.custom_sparql_checks %}
^^^ src/sparql/dc-properties-violation.sparql
# The purpose of this violation is to make sure people update
# from using the deprecated DC Elements 1.1 namespace (http://purl.org/dc/elements/1.1/)
# to using the recommended DC Terms namespace (http://purl.org/dc/terms/)
# See also discussion on https://github.com/oborel/obo-relations/pull/692
SELECT ?term ?predicate WHERE {
?term ?predicate ?value .
FILTER(STRSTARTS(STR(?predicate), "http://purl.org/dc/elements/1.1/"))
FILTER(isIRI(?term) && ({% if project.namespaces %}{% for ns in project.namespaces %}STRSTARTS(str(?term), "{{ ns }}"){% if not loop.last %} || {% endif %}{% endfor %}{% else %}STRSTARTS(str(?term), "{{ project.uribase }}/{{ project.id.upper() }}_"){% endif %}))
}
{% endif %}
{%- if project.components is defined %}
{%- for component in project.components.products %}
^^^ src/ontology/components/{{ component.filename }}
<?xml version="1.0"?>
<rdf:RDF
xml:base="{{ project.uribase }}/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:obo="http://purl.obolibrary.org/obo/">
<owl:Ontology rdf:about="{{ project.uribase }}/{% if project.uribase_suffix is not none %}{{ project.uribase_suffix }}{% else %}{{ project.id }}{% endif %}/components/{{ component.filename }}"/>
<!-- This is a placeholder, it will be regenerated when makefile is first executed -->
</rdf:RDF>
{%- endfor %}
{%- endif %}
{%- if 'basic' in project.release_artefacts or project.primary_release == 'basic' %}
^^^ src/ontology/keeprelations.txt
BFO:0000050
{% endif -%}
{% if project.ci is defined -%}{% if 'travis' in project.ci %}
^^^ .travis.yml
## REMEMBER TO SET UP YOUR GIT REPO FOR TRAVIS
## Go to: https://travis-ci.org/{{ project.github_org }} for details
sudo: required
services:
- docker
before_install:
- docker pull obolibrary/odkfull
# command to run tests
script: cd src/ontology && sh run.sh make test
#after_success:
# coveralls
# whitelist
branches:
only:
- {{ project.git_main_branch }}
- test-travis
### Add your own lists here
### See https://github.com/INCATools/ontology-development-kit/issues/35
notifications:
email:
{% endif -%}{% if (('github_actions' in project.ci) and ('qc' in project.workflows)) %}
^^^ .github/workflows/qc.yml
# Basic ODK workflow
name: CI
# Controls when the action will run.
on:
# Triggers the workflow on push or pull request events but only for the {{ project.git_main_branch }} branch
push:
branches: [ {{ project.git_main_branch }} ]
pull_request:
branches: [ {{ project.git_main_branch }} ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# This workflow contains a single job called "ontology_qc"
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:{% if env is defined -%}{{env['ODK_VERSION'] or "latest" }}{%- else %}latest{% endif %}
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v4
- name: Run ontology QC checks
env:
DEFAULT_BRANCH: {{ project.git_main_branch }}
run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
{% endif -%}{% if 'gitlab-ci' in project.ci %}
^^^ .gitlab-ci.yml
# Basic ODK workflow to run ontology QC checks
ontology_qc:
stage: test
image: obolibrary/odkfull:{% if env is defined -%}{{env['ODK_VERSION'] or "latest" }}{%- else %}latest{% endif %}
# Controls when the job will run.
rules:
# Run on merge request pipelines when a merge request is open for the branch.
# Run on branch pipelines for main when a merge request is not open for the branch.
- if: $CI_PIPELINE_SOURCE == "merge_request_event"
- if: $CI_COMMIT_BRANCH && $CI_OPEN_MERGE_REQUESTS
when: never
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
# Script defines a sequence of tasks that will be executed as part of the job
script:
- cd src/ontology
- make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
{% endif -%}
{% endif -%}
{% if (('github_actions' in project.ci) and ('diff' in project.workflows)) %}
^^^ .github/workflows/diff.yml
name: 'Create ROBOT diffs on Pull requests'
on:
# Triggers the workflow on pull request events for the master branch
pull_request:
branches: [ master ]
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
edit_file:
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "latest" }}{%- else %}latest{% endif %}
steps:
- uses: actions/checkout@v4
# Checks-out main branch under "main" directory
- uses: actions/checkout@v4
with:
ref: master
path: master
- name: Diff classification
run: export ROBOT_JAVA_ARGS=-Xmx6G; robot diff --labels True --left master/src/ontology/{{ project.id }}-edit.{{ project.edit_format }} --left-catalog master/src/ontology/catalog-v001.xml --right src/ontology/{{ project.id }}-edit.{{ project.edit_format }} --right-catalog src/ontology/catalog-v001.xml -f markdown -o edit-diff.md
- name: Upload diff
uses: actions/upload-artifact@v4
with:
name: edit-diff.md
path: edit-diff.md
classify_branch:
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "latest" }}{%- else %}latest{% endif %}
steps:
- uses: actions/checkout@v4
- name: Classify ontology
run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE {{ project.id }}.owl
- name: Upload PR {{ project.id }}.owl
uses: actions/upload-artifact@v4
with:
name: {{ project.id }}-pr.owl
path: src/ontology/{{ project.id }}.owl
retention-days: 1
classify_main:
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "latest" }}{%- else %}latest{% endif %}
steps:
- uses: actions/checkout@v4
with:
ref: master
- name: Classify ontology
run: cd src/ontology; make IMP=FALSE PAT=FALSE MIR=FALSE {{ project.id }}.owl
- name: Upload master {{ project.id }}.owl
uses: actions/upload-artifact@v4
with:
name: {{ project.id }}-master.owl
path: src/ontology/{{ project.id }}.owl
retention-days: 1
diff_classification:
needs:
- classify_branch
- classify_main
runs-on: ubuntu-latest
container: obolibrary/odklite:{% if env is defined -%}{{env['ODK_VERSION'] or "latest" }}{%- else %}latest{% endif %}
steps:
- uses: actions/checkout@v4
- name: Download master classification
uses: actions/download-artifact@v4
with:
name: {{ project.id }}-master.owl
path: src/ontology/{{ project.id }}-master.owl
- name: Download PR classification
uses: actions/download-artifact@v4
with:
name: {{ project.id }}-pr.owl
path: src/ontology/{{ project.id }}-pr.owl
- name: Diff classification
run: export ROBOT_JAVA_ARGS=-Xmx6G; cd src/ontology; robot diff --labels True --left {{ project.id }}-master.owl/{{ project.id }}.owl --left-catalog catalog-v001.xml --right {{ project.id }}-pr.owl/{{ project.id }}.owl --right-catalog catalog-v001.xml -f markdown -o classification-diff.md
- name: Upload diff
uses: actions/upload-artifact@v4
with:
name: classification-diff.md
path: src/ontology/classification-diff.md
post_comment:
needs: [diff_classification, edit_file]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Download reasoned diff
uses: actions/download-artifact@v4
with:
name: classification-diff.md
path: classification-diff.md
- name: Prepare reasoned comment
run: "echo \"<details>\n <summary> Here's a diff of how these changes impact the classified ontology: </summary> \n\" >comment.md; cat classification-diff.md/classification-diff.md >>comment.md"
- name: Post reasoned comment
env:
GITHUB_TOKEN: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
uses: NejcZdovc/[email protected]
with:
file: "../../comment.md"
identifier: "REASONED"
- uses: actions/checkout@v4
- name: Download edit diff
uses: actions/download-artifact@v4
with:
name: edit-diff.md
path: edit-diff.md
- name: Prepare edit file comment
run: "echo \"<details>\n <summary> Here's a diff of your edit file (unreasoned) </summary> \n\" >edit-comment.md; cat edit-diff.md/edit-diff.md >>edit-comment.md"
- name: Post comment
env:
GITHUB_TOKEN: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
uses: NejcZdovc/[email protected]
with:
file: "../../edit-comment.md"
identifier: "UNREASONED"
{% endif -%}
{% if (('github_actions' in project.ci) and ('release-diff' in project.workflows)) %}
^^^ .github/workflows/release-diff.yml
name: Post release diff
on:
# Triggers the workflow on pull request events for the {{ project.git_main_branch }} branch
pull_request:
branches: [ {{ project.git_main_branch }} ]
paths:
- 'src/ontology/reports/release-diff.md'
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
jobs:
post_diff:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Prepare release comment
env:
GITHUB_SHA: {% raw %}${{ github.sha }}{% endraw %}
run: "echo \"[Here's a diff of how this release impacts {{ project.id }}.owl](https://github.com/obophenotype/{{ project.repo }}/blob/${% raw %}${{ env.GITHUB_SHA }}{% endraw %}/src/ontology/reports/release-diff.md)\" >comment.md"
- name: Post reasoned comment
env:
GITHUB_TOKEN: {% raw %}${{ secrets.GITHUB_TOKEN }}{% endraw %}
uses: NejcZdovc/[email protected]
with:
github_token: {% raw %}${{ env.GITHUB_TOKEN }}{% endraw %}
file: "../../comment.md"
identifier: "RELEASE-DIFF"
{% endif -%}
{% if project.use_custom_import_module %}
^^^ src/templates/external_import.tsv
ID Entity Type
ID TYPE
owl:Thing owl:Class
{% endif -%}
{% if project.documentation is not none %}
^^^ docs/index.md
# {{ project.id.upper() }} Ontology Documentation
[//]: # "This file is meant to be edited by the ontology maintainer."
Welcome to the {{ project.id.upper() }} documentation!
You can find descriptions of the standard ontology engineering workflows [here](odk-workflows/index.md).
^^^ docs/cite.md
# How to cite {{ project.id.upper() }}
^^^ docs/contributing.md
# How to contribute to {{ project.id.upper() }}
^^^ docs/odk-workflows/index.md
# Default ODK Workflows
- [Daily Editors Workflow](EditorsWorkflow.md)
- [Release Workflow](ReleaseWorkflow.md)
- [Manage your ODK Repository](RepoManagement.md)
- [Setting up Docker for ODK](SettingUpDockerForODK.md)
- [Imports management](UpdateImports.md)
- [Managing the documentation](ManageDocumentation.md)
- [Managing your Automated Testing](ManageAutomatedTest.md)
^^^ docs/odk-workflows/ContinuousIntegration.md
# Introduction to Continuous Integration Workflows with ODK
Historically, most repos have been using Travis CI for continuous integration testing and building, but due to
runtime restrictions, we recently switched a lot of our repos to GitHub actions. You can set up your repo with CI by adding
this to your configuration file (src/ontology/{{ project.id }}-odk.yaml):
```
ci:
- github_actions
```
When [updateing your repo](RepoManagement.md), you will notice a new file being added: `.github/workflows/qc.yml`.
This file contains your CI logic, so if you need to change, or add anything, this is the place!
Alternatively, if your repo is in GitLab instead of GitHub, you can set up your repo with GitLab CI by adding
this to your configuration file (src/ontology/{{ project.id }}-odk.yaml):
```
ci:
- gitlab-ci
```
This will add a file called `.gitlab-ci.yml` in the root of your repo.
^^^ docs/odk-workflows/EditorsWorkflow.md
# Editors Workflow
The editors workflow is one of the formal [workflows](index.md) to ensure that the ontology is developed correctly according to ontology engineering principles. There are a few different editors workflows:
1. Local editing workflow: Editing the ontology in your local environment by hand, using tools such as Protégé, ROBOT templates or DOSDP patterns.
2. Completely automated data pipeline (GitHub Actions)
3. DROID workflow
This document only covers the first editing workflow, but more will be added in the future