Standardize YAML in ontology metadata frontmatter (OBOFoundry#1985)

* Standardize YAML in ontology metadata frontmatter

This PR does the following:

1. Introduces a Python script util/standardize_metadata.py that sorts and properly indents all of the metadata in all ontology metadata files' frontmatter
2. Adds a unit test to ensure that this metadata is sorted

Why do this? It makes it much easier to programatically edit these files without creating massive diffs (after the massive diff in this PR, at least). There are several ways we might want to automatically maintain these metadata, such as the list of dependencies for each ontology.

* Update tox.ini

* Update aao.md

* Update test_integrity.py

* Modify dumping procedure

* Cleanup

* Set up package for code reuse

* Update config.yamllint

* Add extra examples

* Update standardize_metadata.py

* Cleanup

* Update setup.cfg

Author: cthoyt

.gitignore

@@ -1,7 +1,6 @@
 reports
 util/__pycache__/
 util/principles/__pycache__/
-build/
 .jekyll-cache/
 .DS_Store
 /_site
@@ -12,3 +11,22 @@ build/
 tmp/
 *.tmp
 .venv
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST

ontology/aao.md

@@ -5,12 +5,12 @@ title: Amphibian gross anatomy
 contact:
   email: [email protected]
   label: David Blackburn
-taxon:
-  id: NCBITaxon:8292
-  label: Amphibia
 homepage: http://github.com/seger/aao
 is_obsolete: true
 replaced_by: uberon
+taxon:
+  id: NCBITaxon:8292
+  label: Amphibia
 activity_status: inactive
 ---
 

ontology/ado.md

@@ -4,22 +4,22 @@ id: ado
 title: Alzheimer's Disease Ontology
 contact:
   email: [email protected]
-  label: Alpha Tom Kodamullil
   github: akodamullil
+  label: Alpha Tom Kodamullil
   orcid: 0000-0001-9896-3531
+dependencies:
+- id: bfo
 description: Alzheimer's Disease Ontology is a knowledge-based ontology that encompasses varieties of concepts related to Alzheimer'S Disease, structured by upper level Basic Formal Ontology(BFO). This Ontology is enriched by the interrelated entities that demonstrate the network of the understanding on Alzheimer's disease and can be readily applied for text mining.
 domain: health
 homepage: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
-products:
-  - id: ado.owl
-dependencies:
-  - id: bfo
-tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues
 license:
-  url: https://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0
-repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
+  url: https://creativecommons.org/licenses/by/4.0/
 preferredPrefix: ADO
+products:
+- id: ado.owl
+repository: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO
+tracker: https://github.com/Fraunhofer-SCAI-Applied-Semantics/ADO/issues
 activity_status: active
 ---
 

ontology/aeo.md

@@ -1,27 +1,27 @@
 ---
 layout: ontology_detail
 id: aeo
+title: Anatomical Entity Ontology
+build:
+  checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git
+  method: vcs
+  path: src/ontology
+  system: git
 contact:
   email: [email protected]
   label: Jonathan Bard
-license:
-  url: https://creativecommons.org/licenses/by/4.0/
-  label: CC BY 4.0
 description: AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology
 domain: anatomy and development
 homepage: https://github.com/obophenotype/human-developmental-anatomy-ontology/
-tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
+license:
+  label: CC BY 4.0
+  url: https://creativecommons.org/licenses/by/4.0/
+preferredPrefix: AEO
 products:
-  - id: aeo.owl
-title: Anatomical Entity Ontology
-build:
-  checkout: git clone https://github.com/obophenotype/human-developmental-anatomy-ontology.git
-  system: git
-  path: src/ontology
-  method: vcs
-activity_status: inactive
+- id: aeo.owl
 repository: https://github.com/obophenotype/human-developmental-anatomy-ontology
-preferredPrefix: AEO
+tracker: https://github.com/obophenotype/human-developmental-anatomy-ontology/issues
+activity_status: inactive
 ---
 
 The AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology, to about 160 classes using the is_a relationship; it thus provides a detailed type classification for tissues. The ~100 new classes were chosen for their use in categorizing the major vertebrate and invertebrate anatomy ontologies at a granularity adequate for tissues of a single cell type. This site is to be used for posting details of the ontologies and updates

ontology/aero.md

@@ -1,23 +1,23 @@
 ---
 layout: ontology_detail
 id: aero
+title: Adverse Event Reporting Ontology
+build:
+  method: owl2obo
+  source_url: http://purl.obolibrary.org/obo/aero.owl
 contact:
-  orcid: 0000-0002-9551-6370
   email: [email protected]
   label: Melanie Courtot
+  orcid: 0000-0002-9551-6370
 description: The Adverse Event Reporting Ontology (AERO) is an ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events
-license:
-  url: http://creativecommons.org/licenses/by/3.0/
-  label: CC BY 3.0
 domain: health
 homepage: http://purl.obolibrary.org/obo/aero
 is_obsolete: true
+license:
+  label: CC BY 3.0
+  url: http://creativecommons.org/licenses/by/3.0/
 products:
-  - id: aero.owl
-title: Adverse Event Reporting Ontology
-build:
-  source_url: http://purl.obolibrary.org/obo/aero.owl
-  method: owl2obo
+- id: aero.owl
 activity_status: inactive
 ---
 

ontology/agro.md

@@ -2,57 +2,57 @@
 layout: ontology_detail
 id: agro
 title: Agronomy Ontology
-license:
-  url: https://creativecommons.org/licenses/by/4.0/
-  label: CC BY 4.0
-domain: agriculture
-tags:
-  - agronomy
 build:
   checkout: git clone  https://github.com/AgriculturalSemantics/agro.git
+  path: .
   system: git
-  path: "."
-description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments
-homepage: https://github.com/AgriculturalSemantics/agro
 contact:
   email: [email protected]
+  github: marieALaporte
   label: Marie-Angélique Laporte
-  github: "marieALaporte"
   orcid: 0000-0002-8461-9745
+dependencies:
+- id: envo
+- id: go
+- id: foodon
+- id: ncbitaxon
+- id: pato
+- id: peco
+- id: po
+- id: to
+- id: ro
+- id: bfo
+- id: iao
+- id: obi
+- id: uo
+- id: xco
+description: Ontology of agronomic practices, agronomic techniques, and agronomic variables used in agronomic experiments
+domain: agriculture
+homepage: https://github.com/AgriculturalSemantics/agro
+jobs:
+- id: https://travis-ci.org/AgriculturalSemantics/agro
+  type: travis-ci
+license:
+  label: CC BY 4.0
+  url: https://creativecommons.org/licenses/by/4.0/
+preferredPrefix: AGRO
 products:
-  - id: agro.owl
-    title: "AgrO"
-    description: "Contains all AgrO terms and links to other relavent ontologies."
+- id: agro.owl
+  title: AgrO
+  description: Contains all AgrO terms and links to other relavent ontologies.
 publications:
-  - id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
-    title: "Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics."
-usages:
-  - user: https://agrofims.org/about
-    description: AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO.
-  - user: https://gardian.bigdata.cgiar.org/
-    description: AgrO is being used by GARDIAN to facilitate data search within publications and datasets for use in quantitative analyses.
-jobs:
-  - id: https://travis-ci.org/AgriculturalSemantics/agro
-    type: travis-ci
+- id: http://ceur-ws.org/Vol-1747/IT205_ICBO2016.pdf
+  title: 'Data-driven Agricultural Research for Development: A Need for Data Harmonization Via Semantics.'
+repository: https://github.com/AgriculturalSemantics/agro
+tags:
+- agronomy
 tracker: https://github.com/AgriculturalSemantics/agro/issues/
+usages:
+- description: AgroFIMS enables digital collection of agronomic data that is semantically described a priori with agronomic terms from AgrO.
+  user: https://agrofims.org/about
+- description: AgrO is being used by GARDIAN to facilitate data search within publications and datasets for use in quantitative analyses.
+  user: https://gardian.bigdata.cgiar.org/
 activity_status: active
-repository: https://github.com/AgriculturalSemantics/agro
-dependencies:
-  - id: envo
-  - id: go
-  - id: foodon
-  - id: ncbitaxon
-  - id: pato
-  - id: peco
-  - id: po
-  - id: to
-  - id: ro
-  - id: bfo
-  - id: iao
-  - id: obi
-  - id: uo
-  - id: xco
-preferredPrefix: AGRO
 ---
 
 AgrO, the Agronomy Ontology, describes agronomic practices, techniques, and variables used in agronomic experiments. AgrO is being built using traits identified by agronomists, the ICASA variables, and other existing ontologies such as ENVO, UO, PATO, IAO, and CHEBI. Further, AgrO powers AgroFIMS, the Agronomy Fieldbook and Information Management System modeled on a CGIAR Breeding Management System to capture agronomic data.

ontology/aism.md

@@ -4,32 +4,32 @@ id: aism
 title: Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)
 build:
   checkout: git clone https://github.com/insect-morphology/aism
+  path: .
   system: git
-  path: "."
 contact:
   email: [email protected]
-  label: Jennifer C. Girón
   github: JCGiron
+  label: Jennifer C. Girón
   orcid: 0000-0002-0851-6883
+dependencies:
+- id: ro
+- id: uberon
+- id: caro
+- id: pato
+- id: bfo
+- id: bspo
 description: The AISM contains terms used in insect biodiversity research for describing structures of the exoskeleton and the skeletomuscular system. It aims to serve as the basic backbone of generalized terms to be expanded with order-specific terminology.
 domain: anatomy and development
 homepage: https://github.com/insect-morphology/aism
-products:
-  - id: aism.owl
-  - id: aism.obo
-  - id: aism.json
-dependencies:
-  - id: ro
-  - id: uberon
-  - id: caro
-  - id: pato
-  - id: bfo
-  - id: bspo
-tracker: https://github.com/insect-morphology/aism/issues
 license:
-  url: https://creativecommons.org/licenses/by/4.0/
   label: CC BY 4.0
-activity_status: active
-repository: https://github.com/insect-morphology/aism
+  url: https://creativecommons.org/licenses/by/4.0/
 preferredPrefix: AISM
+products:
+- id: aism.owl
+- id: aism.obo
+- id: aism.json
+repository: https://github.com/insect-morphology/aism
+tracker: https://github.com/insect-morphology/aism/issues
+activity_status: active
 ---

ontology/amphx.md

@@ -4,28 +4,28 @@ id: amphx
 title: The Amphioxus Development and Anatomy Ontology
 build:
   checkout: git clone https://github.com/EBISPOT/amphx_ontology.git
+  path: .
   system: git
-  path: "."
 contact:
   email: [email protected]
-  label: Hector Escriva
   github: hescriva
+  label: Hector Escriva
   orcid: 0000-0001-7577-5028
+dependencies:
+- id: uberon
 description: An ontology for the development and anatomy of Amphioxus (Branchiostoma lanceolatum).
 domain: anatomy and development
 homepage: https://github.com/EBISPOT/amphx_ontology
-products:
-  - id: amphx.owl
-  - id: amphx.obo
-dependencies:
-  - id: uberon
-tracker: https://github.com/EBISPOT/amphx_ontology/issues
 license:
-  url: http://creativecommons.org/licenses/by/3.0/
   label: CC BY 3.0
-activity_status: active
-repository: https://github.com/EBISPOT/amphx_ontology
+  url: http://creativecommons.org/licenses/by/3.0/
 preferredPrefix: AMPHX
+products:
+- id: amphx.owl
+- id: amphx.obo
+repository: https://github.com/EBISPOT/amphx_ontology
+tracker: https://github.com/EBISPOT/amphx_ontology/issues
+activity_status: active
 ---
 
 The Amphioxus Development and Anatomy Ontology (AMPHX) is to describe the anatomy and development of Amphioxus, also known as lancelet, member of the invertebrate subphylum Cephalochordata and the phylum Chordata. This ontology is intended to be used for description of gene expression in amphioxus (e.g. Insitus, RNA-seq). The ontology was created in the context of the European project CORBEL (https://www.corbel-project.eu/home.html), and used in the database MARIMBA (http://marimba.obs-vlfr.fr/home).

ontology/apo.md

@@ -1,32 +1,32 @@
 ---
 layout: ontology_detail
 id: apo
+title: Ascomycete phenotype ontology
+build:
+  method: obo2owl
+  source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo
 contact:
   email: [email protected]
-  label: Stacia R Engel
   github: srengel
+  label: Stacia R Engel
   orcid: 0000-0001-5472-917X
-tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues
-license:
-  url: https://creativecommons.org/licenses/by/4.0/
-  label: CC BY 4.0
 description: A structured controlled vocabulary for the phenotypes of Ascomycete fungi
 domain: phenotype
 homepage: http://www.yeastgenome.org/
+license:
+  label: CC BY 4.0
+  url: https://creativecommons.org/licenses/by/4.0/
+preferredPrefix: APO
 products:
-  - id: apo.owl
-  - id: apo.obo
+- id: apo.owl
+- id: apo.obo
+publications:
+- id: https://www.ncbi.nlm.nih.gov/pubmed/20157474
+  title: New mutant phenotype data curation system in the Saccharomyces Genome Database
+repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
 taxon:
   id: NCBITaxon:4890
   label: Ascomycota
-title: Ascomycete phenotype ontology
-build:
-  source_url: https://raw.githubusercontent.com/obophenotype/ascomycete-phenotype-ontology/master/apo.obo
-  method: obo2owl
+tracker: https://github.com/obophenotype/ascomycete-phenotype-ontology/issues
 activity_status: active
-repository: https://github.com/obophenotype/ascomycete-phenotype-ontology
-preferredPrefix: APO
-publications:
-  - id: https://www.ncbi.nlm.nih.gov/pubmed/20157474
-    title: "New mutant phenotype data curation system in the Saccharomyces Genome Database"
 ---