Merge pull request #165 from opentargets/ds_consolidating_repo

refactor: re-organizing the repo

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: check-json
+      - id: check-yaml
+      - id: pretty-format-json
+        args:
+          - --autofix
+          - --no-ensure-ascii
+          - --no-sort-keys
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.22.0
+    hooks:
+      - id: check-metaschema
+        name: "Validating schema definition against draft schemas"
+        files: ^schemas/.*json$
+        types: [json]

.travis.yml

@@ -1,13 +1,8 @@
 language: python
 python:
-  - "3.6"
+  - "3.8"
 install:
-  - pip install git+https://github.com/Julian/jsonschema.git@v3.0.2#egg=jsonschema
+  - pip install git+https://github.com/python-jsonschema/check-jsonschema.git@0.20.0#egg=check-jsonschema
   - wget -O draft7.json http://json-schema.org/draft-07/schema
-  - wget -O draft4.json http://json-schema.org/draft-04/schema
 script:
-  - jsonschema -i opentargets_chemical_probe.json draft7.json
-  - jsonschema -i opentargets_target_safety.json draft7.json 
-  - jsonschema -i opentargets_tep.json draft7.json
-  - jsonschema -i opentargets.json draft7.json
-  - jsonschema -i OT_network_schema.json draft4.json
+  - for f in $(ls schemas/*json); do check-jsonschema --schemafile draft7.json  $f ;done

README.md

@@ -0,0 +1,22 @@
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/opentargets/json_schema/master.svg)](https://results.pre-commit.ci/latest/github/opentargets/json_schema/master)
+
+# Schemas of the OpenTargets Platform data models
+
+This repository contains schema definitions of some of the data models the OpenTargets Platform deals with.
+Either as an input or generates as an output.
+
+**Folders**:
+
+- `/schemas/` - List of schemas in JSON format.
+- `/pydantic_models/` - Definitions of the data models using Python's [Pydantic](https://docs.pydantic.dev/) tool. [jsontopydantic](https://jsontopydantic.com/) is helpful for the purpose of defining a JSON schema as a Pydantic model. While it may require some customization, it streamlines the majority of the Pydantic boilerplate.
+
+## Available schemas
+
+- `TEP.json`: Description of [Target Enabling Packages](https://platform-docs.opentargets.org/target/chemical-probes-and-teps#target-enabling-packages).
+- `chemical_probes.json`: Description of the [chemical probes](https://platform-docs.opentargets.org/target/chemical-probes-and-teps#chemical-probes) data model.
+- `disease_target_evidence.json`: Description of disease-target evidence input. Separate schemas are defined for each data sources.
+- `target_safety.json`: Description of [target safety](https://platform-docs.opentargets.org/target/safety).
+- `molecular_interactions.json`: Definition of the [molecular interactions](https://platform-docs.opentargets.org/target/molecular-interactions) input.
+- `molecular_interactions-output.json`: Definition for the molecular interactions dataset generated by the Platform ETL.
+
+##

pydantic_models/chemical_probes.py

@@ -49,6 +49,6 @@ def validator(item):
         return False
 
     return True
-    
+
 print(validator(ex))
-print(ChemicalProbes.schema_json(indent=2))
+print(ChemicalProbes.schema_json(indent=2))

pydantic_models/target_safety_liabilities.py

@@ -43,7 +43,7 @@ class Study(BaseModel):
 
     description: Optional[str] = Field(description='Description of the study.')
     name: Optional[str] = Field(description='Name of the study.', examples='ACEA_ER_80hr')
-    type: Optional[str] = Field(description='Conceptual biological and/or chemical features of the study.', examples='cell-based')        
+    type: Optional[str] = Field(description='Conceptual biological and/or chemical features of the study.', examples='cell-based')
     class Config:
         extra = Extra.forbid
         anystr_strip_whitespace = True
@@ -86,6 +86,6 @@ def validator(item):
         return False
 
     return True
-    
+
 print(validator(ex))
-print(TargetSafety.schema_json(indent=2))
+print(TargetSafety.schema_json(indent=2))