_dynamic_files.jinja2

{#-

  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" %}
{% if project.import_group is defined -%}
{% for imp in project.import_group.products %}
import: http://purl.obolibrary.org/obo/{{ project.id }}/imports/{{ imp.id }}_import.owl
{% endfor %}
{% endif %}
{%- if project.use_dosdps %}
import: http://purl.obolibrary.org/obo/{{ project.id }}/patterns/definitions.owl
{%- if project.import_pattern_ontology %}
import: http://purl.obolibrary.org/obo/{{ project.id }}/patterns/pattern.owl
{% endif -%}
{% endif %}
ontology: {{project.id}}
property_value: http://purl.org/dc/elements/1.1/description "{{ project.description }}" xsd:string
property_value: http://purl.org/dc/elements/1.1/title "{{ project.title }}" xsd:string
property_value: http://purl.org/dc/terms/license {{ project.license }}

[Term]
id: {{ project.id | upper }}:00000000
name: root node

{% else %}
Prefix(:=<http://purl.obolibrary.org/obo/{{ project.id }}.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#>)
Prefix(dce:=<http://purl.org/dc/elements/1.1/>)
Prefix(dcterms:=<http://purl.org/dc/terms/>)


Ontology(<http://purl.obolibrary.org/obo/{{ project.id }}.owl>
{% if project.import_group is defined -%}
{% for imp in project.import_group.products %}
Import(<http://purl.obolibrary.org/obo/{{ project.id }}/imports/{{ imp.id }}_import.owl>)
{% endfor %}
{% endif %}

{%- if project.use_dosdps %}
Import(<http://purl.obolibrary.org/obo/{{ project.id }}/patterns/definitions.owl>)
{%- if project.import_pattern_ontology %}
Import(<http://purl.obolibrary.org/obo/{{ project.id }}/patterns/pattern.owl>)
{% endif -%}
{% endif %}

Annotation(dce:title "{{ project.title }}")
Annotation(dcterms:license <{{ project.license }}>)
Annotation(dce:description "{{ project.description }}")

Declaration(Class(<http://purl.obolibrary.org/obo/{{ project.id | upper }}_00000000>))


############################
#   Classes
############################

# Class: <http://purl.obolibrary.org/obo/{{ project.id | upper }}_00000000>

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/{{ project.id | upper }}_00000000> "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: dc: <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: <http://purl.obolibrary.org/obo/{{ project.id }}/{{ project.id }}-idranges.owl>


Annotations: 
    idsfor: "{{ project.id | upper }}",
    idprefix: "http://purl.obolibrary.org/obo/{{ 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

{#-

  Imports files, one per import

#}
{% for imp in project.import_group.products %}
^^^ src/ontology/imports/{{ imp.id }}_import.owl
<?xml version="1.0"?>
<rdf:RDF 
     xml:base="http://purl.obolibrary.org/obo/"
     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 }}/{{ project.id }}/imports/{{ imp.id }}_import.owl"/>

    <!-- This is a placeholder, it will be regenerated when makefile is first executed -->
</rdf:RDF>
{#-

  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

#}
^^^ src/ontology/imports/{{ imp.id }}_terms.txt
{%- if imp.id == 'ro' %}
BFO:0000050
RO:0002202
{%- elif imp.id == 'bfo' %}
BFO:0000040
{%- elif imp.id == 'go' %}
GO:0008150
{%- elif imp.id == 'uberon' %}
UBERON:0001062
{%- elif imp.id == 'cl' %}
CL:0000000
{%- elif imp.id == 'pato' %}
PATO:0000001
{%- elif imp.id == 'mpath' %}
MPATH:0
{%- elif imp.id == 'doid' %}
DOID:4
{%- elif imp.id == 'ncbitaxon' %}
NCBITaxon:1
{%- elif imp.id == 'chebi' %}
CHEBI:24431
{%- elif imp.id == 'bco' %}
http://purl.obolibrary.org/obo/BCO_0000081
{%- elif imp.id == 'envo' %}
ENVO:00001998
{%- elif imp.id == 'iao' %}
IAO:0000577
{%- elif imp.id == 'uo' %}
UO:0010003
{%- elif imp.id == 'obi' %}
OBI:0000011
{%- elif imp.id == 'hsapdv' %}
http://purl.obolibrary.org/obo/HsapDv_0000000
{%- elif imp.id == 'nbo' %}
NBO:0000313
{%- else %}
{{ imp.id|upper }}:0000000
{{ imp.id|upper }}:0000001
{{ imp.id|upper }}:0000002
{%- endif %}
{% 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.

#}
^^^ 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 }}/master/{{ project.id }}.owl
- {{ project.id }}.obo: https://raw.githubusercontent.com/{{ project.github_org }}/{{ project.repo }}/master/{{ 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 }}/master/
{#-
    Example pattern implementation TSV
#}
{%- if project.use_dosdps %}
^^^ 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 %}
{#-
    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) && (regex(str(?term), UCASE("{{ project.id }}_")){% if project.namespaces %}{% for ns in project.namespaces %} || regex(str(?term), "{{ ns }}"){% endfor %}{% 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="http://purl.obolibrary.org/obo/"
     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 }}/{{ project.id }}/components/{{ component.filename }}"/>

    <!-- This is a placeholder, it will be regenerated when makefile is first executed -->
</rdf:RDF>
{%- endfor %}
{%- endif %}