feat: Add ability to accept multi word gene_id

.github/workflows/python-test.yml

@@ -5,33 +5,32 @@ name: Test
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main"]
   pull_request:
-    branches: [ "main" ]
+    branches: ["main"]
 
 permissions:
   contents: read
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.12
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.12"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install ruff pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with ruff
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        ruff check --output-format=github .
-    - name: Test with pytest
-      run: |
-        python -m pytest tests
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pre-commit pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Install pre-commit hooks
+        run: pre-commit install
+      - name: Run pre-commit hooks for linting and other checks
+        run: pre-commit run --all-files
+      - name: Test with pytest
+        run: |
+          python -m pytest tests

.pre-commit-config.yaml

@@ -3,6 +3,13 @@
 
 default_stages: [pre-commit]
 repos:
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: "v3.8.1" # Use the sha / tag you want to point at
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - prettier@2.1.2
+          - "@prettier/plugin-xml@0.12.0"
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
@@ -19,6 +26,6 @@ repos:
     hooks:
       # Run the linter.
       - id: ruff-check
-        args: [ --fix ]
+        args: [--fix]
       # Run the formatter.
       - id: ruff-format

README.md

@@ -1,2 +1,3 @@
 # Rule-Parser
+
 DRAM LARK based Rule Parser for misciellaneous rules parsing tasks such as traits, summarize, and product.

src/rules.lark

@@ -36,8 +36,11 @@ list_lit: "[" expr ("," expr)+ "]"   -> step_
 
 name_ref: IDENT ":" IDENT                 -> qualified_name
         | IDENT                           -> simple_name
+        | BTICK_NAME                      -> quoted_name
+        | IDENT ":" BTICK_NAME            -> quoted_name
 
 IDENT: /[A-Za-z0-9_\-\.]+/
+BTICK_NAME: /`([^`\\]|\\.)*`/
 NUMBER: /[0-9]+(\.[0-9]+)?/
 STRING: ESCAPED_STRING
 

src/rules.py

@@ -1,16 +1,16 @@
 from __future__ import annotations
 
-import functools
+from dataclasses import dataclass
+from typing import Dict, Tuple, List, Optional, Set, Iterable
 import operator
 import os
-from dataclasses import dataclass
 from pathlib import Path
-from typing import Dict, Iterable, List, Optional, Set, Tuple
+import functools
 
 import networkx as nx
 import numpy as np
 import polars as pl
-from lark import Lark, LarkError, Transformer
+from lark import Lark, Transformer, LarkError
 
 OP_TO_EXPR = {
     "gt": operator.gt,
@@ -71,6 +71,7 @@ class RuleError(Exception):
         .str.split(",")
         .list.eval(pl.element().str.strip_chars().str.split(" ").list.first())
     ),
+    "DEFAULT": lambda col: pl.col(col).cast(pl.Utf8).cast(pl.List(pl.Utf8)),
 }
 
 CALL_FUNCTIONS = {
@@ -264,6 +265,15 @@ def qualified_name(self, items):
         db, value = items
         return Name(value=str(value), db=str(db))
 
+    def quoted_name(self, items):
+        val_index = 0 if (len(items) == 1) else 1
+        items[val_index] = (
+            items[val_index][1:-1].replace(r"\`", "`").replace(r"\\", "\\")
+        )  # remove backticks
+        if len(items) == 2:
+            return self.qualified_name(items)
+        return self.simple_name(items)
+
     def number(self, items):
         return Number(float(str(items[0])))
 
@@ -323,7 +333,7 @@ def from_rules(cls, *args, **kwargs) -> CompiledRules:
         }
 
         # Expand rules using expanded defs
-        # we need to hit again in case defs is empty (no alias col)
+        # we need to hit again in case defs is empty (no parent col)
         # and we still need to add needed features from rules
         features_by_rules = {k: set() for k in rules.keys()}
         trees_by_rules = {k: nx.DiGraph() for k in rules.keys()}
@@ -351,15 +361,15 @@ def load_rules(
     rules_path: str = None,
     rules: pl.LazyFrame = None,
     label_col: str = "name",
-    alias_col: str = "alias",
+    parent_col: str = "alias",
     rules_col: str = "rule",
     allow_visualize_functions: bool = False,
 ) -> Tuple[Dict[str, Expr], Dict[str, Expr]]:
     """
-    Assumes TSV has columns at least: name, rule
+    Assumes TSV has columns at least: name, parent, child
     Convention used here:
-      - if `name` is non-empty: this is an OUTPUT RULE whose expression is in `rule`
-      - if `name` is empty and `alias` is non-empty: this is a DEFINITION macro: alias := rule
+      - if `name` is non-empty: this is an OUTPUT RULE whose expression is in `child`
+      - if `name` is empty and `parent` is non-empty: this is a DEFINITION macro: parent := child
     If your file uses a slightly different convention, adjust this function only.
     """
     assert (rules_path is not None) != (rules is not None), (
@@ -380,7 +390,7 @@ def load_rules(
             f"rules TSV missing required columns {required}. Found: {lf.columns}"
         )
 
-    has_alias_col = alias_col and (alias_col in cols)
+    has_parent_col = parent_col and (parent_col in cols)
 
     with open(Path(__file__).parent.absolute() / "rules.lark") as f:
         parser = Lark(
@@ -431,11 +441,11 @@ def parse_rule_expr(expr_str: str) -> Expr:
     }
 
     definitions = {}
-    if has_alias_col:
+    if has_parent_col:
         definitions = {
             a: b
-            for a, b in lf.filter(~pl.col(alias_col).is_null())
-            .select([pl.col(alias_col), pl.col(rules_col)])
+            for a, b in lf.filter(~pl.col(parent_col).is_null())
+            .select([pl.col(parent_col), pl.col(rules_col)])
             .collect()
             .iter_rows()
         }
@@ -567,7 +577,7 @@ def recurse(expr: Expr, add_name_to_needed: bool = True) -> Expr:
             out = PipeChain(calls=tuple(calls))
         else:
             raise TypeError(expr)
-        # Some nodes need validation and have to be done after rules are expanded
+        # Some nodes need validation and have to be done after children are expanded
         try:
             out.validate()
         except Exception:
@@ -593,8 +603,19 @@ def build_present_map(
     """Build present_map of needed gene_ids from annotations DataFrame"""
     additional_cols = additional_cols or []
     besthit_cols = [col for col in besthit_cols if col in lf.columns]
+    besthit_cols.extend(
+        [
+            col
+            for col in lf.columns
+            if (col.endswith("_id") and col not in besthit_cols and col != "query_id")
+        ]
+    )
     for col in besthit_cols:
-        lf = lf.with_columns(ID_EXPR_DICT[col].alias(col)).explode(col)
+        if col not in ID_EXPR_DICT:
+            explode_col = ID_EXPR_DICT["DEFAULT"](col).alias(col)
+        else:
+            explode_col = ID_EXPR_DICT[col].alias(col)
+        lf = lf.with_columns(explode_col).explode(col)
     lf = lf.select([sample_col] + besthit_cols + additional_cols)
 
     # unpivot to long (sample, hit)
@@ -833,7 +854,7 @@ def not_(x: np.ndarray = None) -> np.ndarray | pl.Expr:
             if isinstance(x, pl.Expr):
                 x = [x]
             masks = x
-            if len(masks) == 0:
+            if len(masks) == 1:
                 mask = masks[0]
             else:
                 mask = masks[0].and_(*[mask for mask in masks[1:]])