Merge pull request #1 from ethho/dev-demo

Demo approaches

.github/workflows/tox.yaml

@@ -23,20 +23,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.7
+      - name: Set up Python 3.11
         uses: actions/setup-python@v2
         with:
-          python-version: '3.7'
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.8'
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.9'
+          python-version: '3.11'
       - name: Install Python dependencies
-        run: python -m pip install -q poetry tox
+        run: |
+          pipx install tox
+          pipx install poetry
       - name: Run all tox tests
         if: github.event_name != 'pull_request'
         run: tox --

datajoint_file_validator/__init__.py

@@ -0,0 +1,3 @@
+from . import (
+    snapshot, validate, manifest, result
+)

datajoint_file_validator/cli.py

@@ -0,0 +1,54 @@
+import typer
+from typing_extensions import Annotated
+from rich import print as rprint
+from rich.console import Console
+from rich.table import Table
+
+console = Console()
+app = typer.Typer()
+
+
+@app.callback()
+def callback():
+    """
+    Welcome to datajoint-file-validator!
+    """
+
+
+@app.command()
+def show_table():
+    table = Table("Name", "Item")
+    table.add_row("Rick", "Portal Gun")
+    table.add_row("Morty", "Plumbus")
+    console.print(table)
+
+
+@app.command()
+def open_file(path: str):
+    """
+    Open a file at PATH in the default app.
+    """
+    rprint(f":left_speech_bubble:  Opening file {path}")
+    typer.launch(path, locate=True)
+
+
+@app.command()
+def read_file(path: Annotated[typer.FileText, typer.Option()]):
+    """
+    Reads lines from a file at PATH.
+    """
+    for line in path:
+        rprint(f"Config line: {path}")
+
+
+@app.command()
+def main(name: str, lastname: str = "", formal: bool = False):
+    """
+    Say hi to NAME, optionally with a --lastname.
+
+    If --formal is used, say hi very formally.
+    """
+    if formal:
+        rprint(f"Good day Ms. {name} {lastname}.")
+    else:
+        rprint(f"Hello {name} {lastname}")

datajoint_file_validator/main.py

@@ -0,0 +1,31 @@
+import yaml
+from cerberus import schema_registry
+from cerberus import rules_set_registry
+
+
+def _example_registry_add():
+    schema_registry.add("non-system user", {"uid": {"min": 1000, "max": 0xFFFF}})
+    schema = {
+        "sender": {"schema": "non-system user", "allow_unknown": True},
+        "receiver": {"schema": "non-system user", "allow_unknown": True},
+    }
+    rules_set_registry.extend(
+        (("boolean", {"type": "boolean"}), ("booleans", {"valuesrules": "boolean"}))
+    )
+    schema = {"foo": "booleans"}
+
+
+def _example_schema_from_yaml():
+    schema_text = """
+    name:
+      type: string
+    age:
+      type: integer
+      min: 10
+    """
+    schema = yaml.safe_load(schema_text)
+    document = {"name": "Little Joe", "age": 5}
+    v.validate(document, schema)
+    # False
+    v.errors
+    # {'age': ['min value is 10']}

datajoint_file_validator/manifest.py

@@ -0,0 +1,31 @@
+from dataclasses import dataclass
+from typing import Dict, List, Any
+from .snapshot import PathLike
+
+Manifest = Any
+
+
+@dataclass
+class Constraint:
+    """A single constraint that evaluates True or False for a fileset."""
+    operator: str
+
+
+@dataclass
+class Rule:
+    """A single rule for a fileset."""
+    name: str
+    description: str
+    root: PathLike
+    constraints: List[Constraint]
+
+
+
+@dataclass
+class Manifest:
+    """Manifest for a fileset, defining a fileset type."""
+
+    name: str
+    version: str
+    description: str
+    rules: List[Rule]

datajoint_file_validator/manifests/demo_bob_lab_frames_v0.1.yaml

@@ -0,0 +1,46 @@
+id: https://raw.githubusercontent.com/datajoint/datajoint-file-validator/main/manifests/demo_bob_lab_frames_v0.1
+name: bob_lab_frames
+version: 0.1.0
+description: Example of a fileset type for a Bob Lab fileset
+author:
+  name: Ethan Ho
+  email: [email protected]
+rules:
+  - name: num_files_constraint
+    description: Check that there are between 1 and 5 files in the directory
+    count_min: 1
+    count_max: 5
+  - name: num_files_per_subdir
+    description: >
+      Check that each subdirectory has between 1 and 100 files
+      and that subdirectories only contain .mp4 files.
+    query:
+      path: "/*"
+      type: directory
+    rules:
+      - name: count_per_subdir
+        # Here, the query ("/**") is relative to the sub-directory
+        # instead of the root.
+        query: "/"
+        count_min: 1
+        count_max: 100
+      - name: check_file_type
+        # query: "/**" is implicit here
+        regex: "^.*\\.mp4$"
+  - name: file_type_in_subdir
+    description: Check that each subdirectory has exactly one obs.md file
+    query:
+      # Instead of path, regex, or type, we can write a custom query function
+      # that filters the items that are passed to the constraints.
+      eval: |
+        def get_subdirs(results: list[dict]) -> list[bool]:
+          return [True for r in results if r['type'] == 'directory' else False]
+    rules:
+      - query: "/obs.md"
+        description: "There is exactly one obs.md"
+      - query: "obs.md"
+        description: "Another way to write the above"
+      - query: "obs.md"
+        description: "Yet another way to write this rule"
+        count_min: 1
+        count_max: 1

datajoint_file_validator/manifests/demo_dlc_v0.1.yaml

@@ -0,0 +1,42 @@
+id: https://raw.githubusercontent.com/datajoint/datajoint-file-validator/main/manifests/demo_dlc_v0.1
+name: demo_dlc
+version: 0.1.0
+description: DeepLabCut demo fileset type
+author:
+  name: Ethan Ho
+  email: [email protected]
+rules:
+  - name: "Min total files"
+    description: "Check that there are at least 6 files anywhere in the fileset"
+    # This is the default query, which returns every file, even if it is in
+    # a subdirectory.
+    query: "/**"
+    count_min: 6
+  - name: "Count .mp4 files"
+    description: "Check that there are at least 4 .mp4 files and their total size is at least 2.0K"
+    query: "/**/*.mp4"
+    # This rule has two constraints, which both must be satisfied for the rule
+    # to pass.
+    count_min: 4
+    total_size_min: 2.0K
+
+  # More complex rules below
+  - name: "Only .mp4 and .csv at top level"
+    # This query returns only files at the top level, and will not consider
+    # files in subdirectories.
+    query: "/*"
+    # Note that this regex will not match subdirectores.
+    regex: ".*\\.mp4$|.*\\.csv$"
+  - name: "Every video file must have a corresponding csv file"
+    description: "Check that every video file has a corresponding csv file"
+    # query: "/**" is implicit here
+    # Instead of other constraints, we can use eval to write a custom constraint function.
+    eval: |
+      def check_one_to_one(results: list[dict]) -> bool:
+          n_mp4 = len([r for r in results if r['extension'] == 'mp4'])
+          n_csv = len([r for r in results if r['extension'] == 'csv'])
+          return n_mp4 == n_csv
+  - name: "Size constraints"
+    description: "Check that the size of all files are within a certain range"
+    total_size_min: 2.0K
+    total_size_max: 10000

datajoint_file_validator/manifests_schemas/v0.1.0.yaml

@@ -0,0 +1,81 @@
+id:
+  type: string
+  required: true
+name:
+  type: string
+  required: true
+version:
+  type: string
+  required: true
+description:
+  type: string
+  required: true
+author:
+  type: dict
+  schema:
+    name:
+      type: string
+      required: true
+    email:
+      type: string
+      required: true
+  required: true
+rules:
+  type: dict
+  schema:
+    num_files_constraint:
+      type: dict
+      schema:
+        query:
+          type: string
+          required: true
+        count_min:
+          type: integer
+          required: true
+        count_max:
+          type: integer
+          required: true
+      required: true
+    num_files_per_subdir:
+      type: dict
+      schema:
+        description:
+          type: string
+          required: true
+        query:
+          type: string
+          required: true
+        rules:
+          type: list
+          schema:
+            type: dict
+            schema:
+              name:
+                type: string
+                required: true
+              query:
+                type: string
+                required: true
+              count_min:
+                type: integer
+                required: true
+              count_max:
+                type: integer
+                required: true
+          required: true
+      required: true
+    file_type_in_subdir:
+      type: dict
+      schema:
+        description:
+          type: string
+          required: true
+        query:
+          type: dict
+          schema:
+            eval:
+              type: string
+              required: true
+          required: true
+      required: true
+  required: true

datajoint_file_validator/result.py

@@ -0,0 +1,13 @@
+from dataclasses import dataclass
+from typing import Dict, Any
+import cerberus
+
+
+@dataclass
+class ValidationResult:
+    status: bool
+    errors: Any
+
+    @classmethod
+    def from_validator(cls, v: cerberus.Validator):
+        return cls(status=v.status, errors=v.errors)