Merge branch 'feature/config_schema_documentary' into develop

docs/change-log.md

@@ -4,6 +4,7 @@
 - Add support for Empatica devices (all sensors)
 - Add logo
 - Move Citation page to the Setup section
+- Add `config.yaml` validation schema and documentation.
 ## v0.4.3
 - Fix bug when any of the rows from any sensor do not belong a time segment
 ## v0.4.2

docs/developers/validation-schema-config.md

@@ -0,0 +1,178 @@
+# Validation schema of `config.yaml`
+
+!!! hint "Why do we need to validate the `config.yaml`?"
+    Most of the key/values in the `config.yaml` are constrained to a set of possible values or types. For example `[TIME_SEGMENTS][TYPE]` can only be one of `["FREQUENCY", "PERIODIC", "EVENT"]`, and `[TIMEZONE]` has to be a string. 
+    
+    We should show the user an error if that's not the case. We could validate this in Python or R but since we reuse scripts and keys in multiple places, tracking these validations can be time consuming and get out of control. Thus, we do these validations through a schema and check that schema before RAPIDS starts processing any data so the user can see the error right away.
+
+    Keep in mind these validations can only cover certain base cases. Some validations that require more complex logic should still be done in the respective script. For example, we can check that a CSV file path actually ends in `.csv` but we can only check that the file actually exists in a Python script.
+ 
+The structure and values of the `config.yaml` file are validated using a YAML schema stored in `tools/config.schema.yaml`. Each key in `config.yaml`, for example `PIDS`, has a corresponding entry in the schema where we can validate its type, possible values, required properties, min and max values, among other things. 
+
+The `config.yaml` is validated against the schema every time RAPIDS runs (see the top of the `Snakefile`):
+
+```python
+validate(config, "tools/config.schema.yaml")
+```
+
+## Structure of the schema
+
+The schema has three main sections `required`, `definitions`, and `properties`. All of them are just nested key/value YAML pairs, where the value can be a primitive type (`integer`, `string`, `boolean`, `number`) or can be another key/value pair (`object`).
+
+### required
+`required` lists `properties` that should be present in the `config.yaml`. We will almost always add every `config.yaml` key to this list (meaning that the user cannot delete any of those keys like `TIMEZONE` or `PIDS`). 
+
+### definitions
+`definitions` lists key/values that are common to different `properties` so we can reuse them. You can define a key/value under `definitions` and use `$ref` to refer to it in any `property`. 
+
+For example, every sensor like `[PHONE_ACCELEROMETER]` has one or more providers like `RAPIDS` and `PANDA`, these providers have some common properties like the `COMPUTE` flag or the `SRC_FOLDER` string, therefore we define a common provider "template" that is used by every provider and extended with properties exclusive to each one of them. For example:
+
+=== "provider definition (template)"
+    The `PROVIDER` definition will be used later on different `properties`.
+
+    ```yaml
+    PROVIDER:
+        type: object
+        required: [COMPUTE, SRC_FOLDER, SRC_LANGUAGE, FEATURES]
+        properties:
+        COMPUTE:
+            type: boolean
+        FEATURES:
+            type: [array, object]
+        SRC_FOLDER:
+            type: string
+        SRC_LANGUAGE:
+            type: string
+            enum: [python, r]
+    ```
+
+=== "provider reusing and extending the template"
+    Notice that in this example `RAPIDS` (a provider) is using and extending the `PROVIDER` template. The `FEATURES` key is overriding the `FEATURES` key from the `#/definitions/PROVIDER` template but is keeping the validation for `COMPUTE`, `SRC_FOLDER`, and `SRC_LANGUAGE`. For more details about reusing properties go to this [link](http://json-schema.org/understanding-json-schema/structuring.html#reuse)
+
+    ```yaml hl_lines="9 10"
+    PHONE_ACCELEROMETER:
+        type: object
+         # .. other properties
+        PROVIDERS:
+            type: ["null", object]
+            properties:
+            RAPIDS:
+                allOf:
+                - $ref: "#/definitions/PROVIDER"
+                - properties:
+                    FEATURES: 
+                        type: array
+                        uniqueItems: True
+                        items:
+                        type: string
+                        enum: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
+    ```
+
+
+
+### properties
+
+`properties` are nested key/values that describe the different components of our `config.yaml` file. Values can be of one or more primitive types like `string`, `number`, `array`, `boolean` and `null`. Values can also be another key/value pair (of type `object`) that are similar to a dictionary in Python.
+
+For example, the following property validates the `PIDS` of our `config.yaml`. It checks that `PIDS` is an `array` with unique items of type `string`.
+
+```yaml
+PIDS:
+    type: array
+    uniqueItems: True
+    items:
+      type: string
+```
+
+## Modifying the schema
+
+!!! hint "Validating the `config.yaml` during development"
+    If you updated the schema and want to check the `config.yaml` is compliant, you can run the command `snakemake --list-params-changes`. You will see `Building DAG of jobs...` if there are no problems or an error message otherwise (try setting any `COMPUTE` flag to a string like `test` instead of `False/True`).
+    
+    You can use this command without having to configure RAPIDS to process any participants or sensors.
+
+You can validate different aspects of each key/value in our `config.yaml` file:
+
+=== "number/integer"
+    Including min and max values
+    ```yaml
+    MINUTE_RATIO_THRESHOLD_FOR_VALID_YIELDED_HOURS:
+        type: number
+        minimum: 0
+        maximum: 1
+
+    FUSED_RESAMPLED_CONSECUTIVE_THRESHOLD:
+        type: integer
+        exclusiveMinimum: 0
+    ```
+=== "string"
+    Including valid values (`enum`)
+    ```yaml
+    items:
+        type: string
+        enum: ["count", "maxlux", "minlux", "avglux", "medianlux", "stdlux"]
+    ```
+=== "boolean"
+    ```yaml
+    MINUTES_DATA_USED:
+        type: boolean
+    ```
+=== "array"
+    Including whether or not it should have unique values, the type of the array's elements (`strings`, `numbers`) and valid values (`enum`).
+    ```yaml
+    MESSAGES_TYPES:
+        type: array
+        uniqueItems: True
+        items:
+            type: string
+            enum: ["received", "sent"]
+    ```
+=== "object"
+    `PARENT` is an object that has two properties. `KID1` is one of those properties that is in turn another object that will reuse the  `"#/definitions/PROVIDER"` `definition` **AND** also include (extend) two extra properties `GRAND_KID1` of type `array` and `GRAND_KID2` of type `number`. `KID2` is another property of `PARENT` of type `boolean`.
+
+    The schema validation looks like this
+    ```yaml
+    PARENT:
+        type: object
+        properties:
+          KID1:
+            allOf:
+              - $ref: "#/definitions/PROVIDER"
+              - properties:
+                  GRAND_KID1:
+                    type: array
+                    uniqueItems: True
+                  GRAND_KID2:
+                    type: number
+          KID2:
+            type: boolean
+    ```
+
+    The `config.yaml` key that the previous schema validates looks like this:
+    ```yaml
+    PARENT:
+        KID1:
+            # These four come from the `PROVIDER` definition (template)
+            COMPUTE: False
+            FEATURES: [x, y] # an array
+            SRC_FOLDER: "any string"
+            SRC_LANGUAGE: "any string"
+
+            # This two come from the extension
+            GRAND_KID1: [a, b] # an array
+            GRAND_KID2: 5.1 # an number
+         KID2: True # a boolean
+    ```
+
+## Verifying the schema is correct
+We recommend that before you start modifying the schema you modify the `config.yaml` key that you want to validate with an invalid value. For example, if you want to validate that `COMPUTE` is boolean, you set `COMPUTE: 123`. Then create your validation, run `snakemake --list-params-changes` and make sure your validation fails (123 is not `boolean`), and then set the key to the correct value. In other words, make sure it's broken first so that you know that your validation works.
+
+!!! warning
+    **Be careful**. You can check that the schema `config.schema.yaml` has a valid format by running `python tools/check_schema.py`. You will see this message if its structure is correct: `Schema is OK`. However, we don't have a way to detect typos, for example `allOf` will work but `allOF` won't (capital `F`) and it won't show any error. That's why we recommend to start with an invalid key/value in your `config.yaml` so that you can be sure the schema validation finds the problem.
+
+## Useful resources
+
+Read the following links to learn more about what we can validate with schemas. They are based on `JSON` instead of `YAML` schemas but the same concepts apply.
+
+- [Understanding JSON Schemas](http://json-schema.org/understanding-json-schema/index.html)
+- [Specification of the JSON schema we use](https://tools.ietf.org/html/draft-handrews-json-schema-01)

mkdocs.yml

@@ -30,6 +30,7 @@ markdown_extensions:
     - pymdownx.tilde
     - attr_list
     - pymdownx.keys
+    - def_list
 extra:
   version:
     method: mike
@@ -125,6 +126,7 @@ nav:
     - Documentation: developers/documentation.md
     - Testing: developers/testing.md
     - Test cases: developers/test-cases.md
+    - Validation schema of config.yaml: developers/validation-schema-config.md
   - Others:
     - Migrating from beta: migrating-from-old-versions.md
     - Code of Conduct: code_of_conduct.md