Merge branch 'version_4' into master as part of v 4.0.0 release

.travis.yml

@@ -3,5 +3,13 @@ language: python
 # python versions to be used for testing
 python:
    - "3.6"
-
-
+
+install:
+   - pip install -r requirements.txt
+
+script:
+   - cd src
+   # python test.py
+   ## temporary patch
+   - python simple_test.py
+   - python sample_test.py

README.md

@@ -1,9 +1,12 @@
+[![Build Status](https://travis-ci.org/HumanCellAtlas/metadata-schema.svg)](https://travis-ci.org/HumanCellAtlas/metadata-schema)
+
+
 # The Human Cell Atlas Metadata Schema
 
-This repo contains the HCA metadata metadata json schemas.
+This repo contains the HCA metadata JSON schemas.
 
-The **design-principles**  can be read in the [linked google-doc](https://docs.google.com/document/d/1eUVpYDLu2AxmxRw2ZUMM-jpKNxQudJbznNyNRp35nLc/edit?usp=sharing)
+The **design-principles** can be read in the [linked Google Doc](https://docs.google.com/document/d/1eUVpYDLu2AxmxRw2ZUMM-jpKNxQudJbznNyNRp35nLc/edit?usp=sharing).
 
 
-How to contribute is described in [contributing.md](https://github.com/HumanCellAtlas/metadata-schema/blob/master/contributing.md)
+How to contribute is described in [contributing.md](https://github.com/HumanCellAtlas/metadata-schema/blob/master/contributing.md).
 

contributing.md

@@ -2,4 +2,4 @@
 
 This file is a place holder for the update process procedure.
 
-You can read the work in progress in [HCA metadata lifecycle and versioning](https://docs.google.com/document/d/1eUVpYDLu2AxmxRw2ZUMM-jpKNxQudJbznNyNRp35nLc/edit?usp=sharing)
+You can read the work in progress in [HCA metadata lifecycle and versioning](https://docs.google.com/document/d/1eUVpYDLu2AxmxRw2ZUMM-jpKNxQudJbznNyNRp35nLc/edit?usp=sharing).

json_meta_schema/ontology_meta.json

@@ -0,0 +1,35 @@
+{
+  "graph_restriction": {
+    "description": "A JSON schema extension field used to specify which ontology terms are valid for a\n field, based on their graph location.  A graph consists of edges representing \n classification (subClassOf) and simple existential restrictions \n (e.g. eye subClassOf part_of some head).  Graph location is specified via a list \n of objectProperties to follow and a list of grouping classes.  \n All ontologies and OWL entities are specified using CURIEs.  \n CURIE resolution depends on an extenal resolution service (e.g. identifiers.org) \n or JSON-LD mapping file. \n",
+    "type": "object",
+    "required": [
+      "ontologies",
+      "relations",
+      "classes",
+      "include_self",
+      "direct"
+    ],
+    "additionalProperties": false,
+    "properties": {
+      "ontologies": {
+        "description": "A list of valid ontologies.  Each ontology is specified using a CURIE.\n",
+        "type": "array",
+        "items": "string"
+      }
+    },
+    "relations": {
+      "description": "A list of relations (object properties) to use for graph-based term grouping.  Each property is specified using a CURIE. type: array Items: string \n"
+    },
+    "classes": {
+      "description": "A list of grouping classes.  Each class is specified using a CURIE\n   type: array\n   items: string \n"
+    },
+    "include_self": {
+      "description": "A boolean allowing specification of whether the graph query should return the specified grouping classes(es).\n",
+      "type": "boolean"
+    },
+    "direct": {
+      "description": "A bolean specifying return of all descendant classes (False) or direct child classes only (True).\n",
+      "type": "boolean"
+    }
+  }
+}

json_meta_schema/ontology_meta.yaml

@@ -0,0 +1,38 @@
+graph_restriction:
+    description: > 
+        A JSON schema extension field used to specify which ontology terms are valid for a
+         field, based on their graph location.  A graph consists of edges representing 
+         classification (subClassOf) and simple existential restrictions 
+         (e.g. eye subClassOf part_of some head).  Graph location is specified via a list 
+         of objectProperties to follow and a list of grouping classes.  
+         All ontologies and OWL entities are specified using CURIEs.  
+         CURIE resolution depends on an extenal resolution service (e.g. identifiers.org) 
+         or JSON-LD mapping file. 
+    # Question: Should the mapping service or file be specified in schema?
+    type: object
+    required: [ontologies, relations, classes, include_self, direct] # we could potentially make relations optional if subClassOf-only is default.
+    additionalProperties: False
+    properties:
+        ontologies:
+            description: > 
+                A list of valid ontologies.  Each ontology is specified using a CURIE.
+            type: array
+            items: string
+    relations:
+        description: > 
+            A list of relations (object properties) to use for graph-based term grouping.  Each property is specified using a CURIE.
+            type: array
+            Items: string 
+    classes:
+        description: > 
+         A list of grouping classes.  Each class is specified using a CURIE
+            type: array
+            items: string 
+    include_self:
+        description: > 
+            A boolean allowing specification of whether the graph query should return the specified grouping classes(es).
+        type: boolean
+    direct:
+        description: >
+            A bolean specifying return of all descendant classes (False) or direct child classes only (True).
+        type: boolean