Fix notebook sources with NotebookLinter.apply (#3693)

## Changes
Add notebook fixing to `NotebookLinter`
- Implement `Notebook.apply` 
- Call `Notebook.apply` from `FileLiner.apply` for `Notebook` source
container
- Remove legacy `NotebookMigrator`
- Introduce `PythonLinter` to run apply on a AST tree
- Allow to 

### Linked issues

Progresses #3514
Breaks up #3520

### Functionality

- [x] modified existing command: `databricks labs ucx
migrate-local-code`

### Tests

- [x] manually tested
- [x] modified and added unit tests
- [x] modified and added integration tests

src/databricks/labs/ucx/github.py

@@ -0,0 +1,38 @@
+from enum import Enum
+import urllib.parse
+
+
+DOCS_URL = "https://databrickslabs.github.io/ucx/docs/"
+GITHUB_URL = "https://github.com/databrickslabs/ucx"
+
+
+class IssueType(Enum):
+    """The issue type"""
+
+    FEATURE = "Feature"
+    BUG = "Bug"
+    TASK = "Task"
+
+
+def construct_new_issue_url(
+    issue_type: IssueType,
+    title: str,
+    body: str,
+    *,
+    labels: set[str] | None = None,
+) -> str:
+    """Construct a new issue URL.
+
+    References:
+    - https://docs.github.com/en/issues/tracking-your-work-with-issues/using-issues/creating-an-issue#creating-an-issue-from-a-url-query
+    """
+    labels = labels or set()
+    labels.add("needs-triage")
+    parameters = {
+        "type": issue_type.value,
+        "title": title,
+        "body": body,
+        "labels": ",".join(sorted(labels)),
+    }
+    query = "&".join(f"{key}={urllib.parse.quote_plus(value)}" for key, value in parameters.items())
+    return f"{GITHUB_URL}/issues/new?{query}"

src/databricks/labs/ucx/install.py

@@ -48,6 +48,7 @@
 )
 from databricks.sdk.useragent import with_extra
 
+from databricks.labs.ucx.github import DOCS_URL
 from databricks.labs.ucx.__about__ import __version__
 from databricks.labs.ucx.assessment.azure import AzureServicePrincipalInfo
 from databricks.labs.ucx.assessment.clusters import ClusterInfo, PolicyInfo
@@ -218,7 +219,7 @@ def run(
             if isinstance(err.__cause__, RequestsConnectionError):
                 logger.warning(
                     f"Cannot connect with {self.workspace_client.config.host} see "
-                    f"https://github.com/databrickslabs/ucx#network-connectivity-issues for help: {err}"
+                    f"{DOCS_URL}#reference/common_challenges/#network-connectivity-issues for help: {err}"
                 )
             raise err
         return config
@@ -573,7 +574,7 @@ def _create_database(self):
             if "Unable to load AWS credentials from any provider in the chain" in str(err):
                 msg = (
                     "The UCX installation is configured to use external metastore. There is issue with the external metastore connectivity.\n"
-                    "Please check the UCX installation instruction https://github.com/databrickslabs/ucx?tab=readme-ov-file#prerequisites"
+                    f"Please check the UCX installation instruction {DOCS_URL}/installation "
                     "and re-run installation.\n"
                     "Please Follow the Below Command to uninstall and Install UCX\n"
                     "UCX Uninstall: databricks labs uninstall ucx.\n"

src/databricks/labs/ucx/source_code/known.py

@@ -14,6 +14,7 @@
 
 from databricks.labs.blueprint.entrypoint import get_logger
 
+from databricks.labs.ucx.github import GITHUB_URL
 from databricks.labs.ucx.hive_metastore.table_migration_status import TableMigrationIndex
 from databricks.labs.ucx.source_code.base import Advice, CurrentSessionState
 from databricks.labs.ucx.source_code.graph import (
@@ -24,6 +25,7 @@
 from databricks.labs.ucx.source_code.path_lookup import PathLookup
 
 logger = logging.getLogger(__name__)
+KNOWN_URL = f"{GITHUB_URL}/blob/main/src/databricks/labs/ucx/source_code/known.json"
 
 """
 Known libraries that are not in known.json
@@ -282,10 +284,9 @@ class KnownDependency(Dependency):
     """A dependency for known libraries, see :class:KnownList."""
 
     def __init__(self, module_name: str, problems: list[KnownProblem]):
-        known_url = "https://github.com/databrickslabs/ucx/blob/main/src/databricks/labs/ucx/source_code/known.json"
         # Note that Github does not support navigating JSON files, hence the #<module_name> does nothing.
         # https://docs.github.com/en/repositories/working-with-files/using-files/navigating-code-on-github
-        super().__init__(KnownLoader(), Path(f"{known_url}#{module_name}"), inherits_context=False)
+        super().__init__(KnownLoader(), Path(f"{KNOWN_URL}#{module_name}"), inherits_context=False)
         self._module_name = module_name
         self.problems = problems
 

src/databricks/labs/ucx/source_code/linters/base.py

@@ -114,6 +114,35 @@ def lint(self, code: str) -> Iterable[Advice]:
     def lint_tree(self, tree: Tree) -> Iterable[Advice]: ...
 
 
+class PythonFixer(Fixer):
+    """Fix python source code."""
+
+    def apply(self, code: str) -> str:
+        """Apply the changes to Python source code.
+
+        The source code is parsed into an AST tree, and the fixes are applied
+        to the tree.
+        """
+        maybe_tree = MaybeTree.from_source_code(code)
+        if maybe_tree.failure:
+            # Fixing does not yield parse failures, linting does
+            logger.warning(f"Parsing source code resulted in failure `{maybe_tree.failure}`: {code}")
+            return code
+        assert maybe_tree.tree is not None
+        tree = self.apply_tree(maybe_tree.tree)
+        return tree.node.as_string()
+
+    @abstractmethod
+    def apply_tree(self, tree: Tree) -> Tree:
+        """Apply the fixes to the AST tree.
+
+        For Python, the fixes are applied to a Tree so that we
+        - Can chain multiple fixers without transpiling back and forth between
+          source code and AST tree
+        - Can extend the tree with (brought into scope) nodes, e.g. to add imports
+        """
+
+
 class DfsaPyCollector(DfsaCollector, ABC):
 
     def collect_dfsas(self, source_code: str) -> Iterable[DirectFsAccess]:

src/databricks/labs/ucx/source_code/linters/files.py

@@ -17,7 +17,7 @@
 from databricks.labs.ucx.source_code.files import LocalFile
 from databricks.labs.ucx.source_code.graph import Dependency
 from databricks.labs.ucx.source_code.known import KnownDependency
-from databricks.labs.ucx.source_code.linters.base import PythonLinter
+from databricks.labs.ucx.source_code.linters.base import PythonFixer, PythonLinter
 from databricks.labs.ucx.source_code.linters.context import LinterContext
 from databricks.labs.ucx.source_code.linters.imports import SysPathChange, UnresolvedPath
 from databricks.labs.ucx.source_code.notebooks.cells import (
@@ -26,7 +26,6 @@
     RunCell,
     RunCommand,
 )
-from databricks.labs.ucx.source_code.notebooks.loaders import NotebookLoader
 from databricks.labs.ucx.source_code.notebooks.magic import MagicLine
 from databricks.labs.ucx.source_code.notebooks.sources import Notebook
 from databricks.labs.ucx.source_code.path_lookup import PathLookup
@@ -42,7 +41,11 @@ class NotebookLinter:
     """
 
     def __init__(
-        self, notebook: Notebook, path_lookup: PathLookup, context: LinterContext, parent_tree: Tree | None = None
+        self,
+        notebook: Notebook,
+        path_lookup: PathLookup,
+        context: LinterContext,
+        parent_tree: Tree | None = None,
     ):
         self._context: LinterContext = context
         self._path_lookup = path_lookup
@@ -76,6 +79,37 @@ def lint(self) -> Iterable[Advice]:
                 )
         return
 
+    def apply(self) -> None:
+        """Apply changes to the notebook."""
+        maybe_tree = self._parse_notebook(self._notebook, parent_tree=self._parent_tree)
+        if maybe_tree and maybe_tree.failure:
+            logger.warning("Failed to parse the notebook, run linter for more details.")
+            return
+        for cell in self._notebook.cells:
+            try:
+                linter = self._context.linter(cell.language.language)
+            except ValueError:  # Language is not supported (yet)
+                continue
+            fixed_code = cell.original_code  # For default fixing
+            tree = self._python_tree_cache.get((self._notebook.path, cell))  # For Python fixing
+            is_python_cell = isinstance(cell, PythonCell)
+            if is_python_cell and tree:
+                advices = cast(PythonLinter, linter).lint_tree(tree)
+            else:
+                advices = linter.lint(cell.original_code)
+            for advice in advices:
+                fixer = self._context.fixer(cell.language.language, advice.code)
+                if not fixer:
+                    continue
+                if is_python_cell and tree:
+                    # By calling `apply_tree` instead of `apply`, we chain fixes on the same tree
+                    tree = cast(PythonFixer, fixer).apply_tree(tree)
+                else:
+                    fixed_code = fixer.apply(fixed_code)
+            cell.migrated_code = tree.node.as_string() if tree else fixed_code
+        self._notebook.back_up_original_and_flush_migrated_code()
+        return
+
     def _parse_notebook(self, notebook: Notebook, *, parent_tree: Tree) -> MaybeTree | None:
         """Parse a notebook by parsing its cells.
 
@@ -264,50 +298,16 @@ def apply(self) -> None:
         source_container = self._dependency.load(self._path_lookup)
         if isinstance(source_container, LocalFile):
             self._apply_file(source_container)
+        elif isinstance(source_container, Notebook):
+            self._apply_notebook(source_container)
 
     def _apply_file(self, local_file: LocalFile) -> None:
         """Apply changes to a local file."""
         fixed_code = self._context.apply_fixes(local_file.language, local_file.original_code)
         local_file.migrated_code = fixed_code
         local_file.back_up_original_and_flush_migrated_code()
 
-
-class NotebookMigrator:
-    def __init__(self, languages: LinterContext):
-        # TODO: move languages to `apply`
-        self._languages = languages
-
-    def revert(self, path: Path) -> bool:
-        backup_path = path.with_suffix(".bak")
-        if not backup_path.exists():
-            return False
-        return path.write_text(backup_path.read_text()) > 0
-
-    def apply(self, path: Path) -> bool:
-        if not path.exists():
-            return False
-        dependency = Dependency(NotebookLoader(), path)
-        # TODO: the interface for this method has to be changed
-        lookup = PathLookup.from_sys_path(Path.cwd())
-        container = dependency.load(lookup)
-        assert isinstance(container, Notebook)
-        return self._apply(container)
-
-    def _apply(self, notebook: Notebook) -> bool:
-        changed = False
-        for cell in notebook.cells:
-            # %run is not a supported language, so this needs to come first
-            if isinstance(cell, RunCell):
-                # TODO migration data, see https://github.com/databrickslabs/ucx/issues/1327
-                continue
-            if not self._languages.is_supported(cell.language.language):
-                continue
-            migrated_code = self._languages.apply_fixes(cell.language.language, cell.original_code)
-            if migrated_code != cell.original_code:
-                cell.migrated_code = migrated_code
-                changed = True
-        if changed:
-            # TODO https://github.com/databrickslabs/ucx/issues/1327 store 'migrated' status
-            notebook.path.replace(notebook.path.with_suffix(".bak"))
-            notebook.path.write_text(notebook.to_migrated_code())
-        return changed
+    def _apply_notebook(self, notebook: Notebook) -> None:
+        """Apply changes to a notebook."""
+        notebook_linter = NotebookLinter(notebook, self._path_lookup, self._context, self._inherited_tree)
+        notebook_linter.apply()

src/databricks/labs/ucx/source_code/linters/pyspark.py

@@ -6,6 +6,8 @@
 from typing import TypeVar
 
 from astroid import Attribute, Call, Const, Name, NodeNG  # type: ignore
+
+from databricks.labs.ucx.github import IssueType, construct_new_issue_url
 from databricks.labs.ucx.hive_metastore.table_migration_status import TableMigrationIndex, TableMigrationStatus
 from databricks.labs.ucx.source_code.base import (
     Advice,
@@ -20,6 +22,7 @@
 from databricks.labs.ucx.source_code.linters.base import (
     SqlLinter,
     Fixer,
+    PythonFixer,
     PythonLinter,
     DfsaPyCollector,
     TablePyCollector,
@@ -33,7 +36,6 @@
 from databricks.labs.ucx.source_code.linters.from_table import FromTableSqlLinter
 from databricks.labs.ucx.source_code.python.python_ast import (
     MatchingVisitor,
-    MaybeTree,
     Tree,
     TreeHelper,
 )
@@ -170,8 +172,16 @@ def lint(
 
     def apply(self, from_table: FromTableSqlLinter, index: TableMigrationIndex, node: Call) -> None:
         table_arg = self._get_table_arg(node)
-        assert isinstance(table_arg, Const)
-        # TODO locate constant when value is inferred
+        if not isinstance(table_arg, Const):
+            # TODO: https://github.com/databrickslabs/ucx/issues/3695
+            source_code = node.as_string()
+            body = (
+                "# Desired behaviour\n\nAutofix following Python code\n\n"
+                f"``` python\nTODO: Add relevant source code\n{source_code}\n```"
+            )
+            url = construct_new_issue_url(IssueType.FEATURE, "Autofix the following Python code", body)
+            logger.warning(f"Cannot fix the following Python code: {source_code}. Please report this issue at {url}")
+            return
         info = UsedTable.parse(table_arg.value, from_table.schema)
         dst = self._find_dest(index, info)
         if dst is not None:
@@ -393,7 +403,7 @@ def matchers(self) -> dict[str, _TableNameMatcher]:
         return self._matchers
 
 
-class SparkTableNamePyLinter(PythonLinter, Fixer, TablePyCollector):
+class SparkTableNamePyLinter(PythonLinter, PythonFixer, TablePyCollector):
     """Linter for table name references in PySpark
 
     Examples:
@@ -427,21 +437,15 @@ def lint_tree(self, tree: Tree) -> Iterable[Advice]:
             assert isinstance(node, Call)
             yield from matcher.lint(self._from_table, self._index, self._session_state, node)
 
-    def apply(self, code: str) -> str:
-        maybe_tree = MaybeTree.from_source_code(code)
-        if not maybe_tree.tree:
-            assert maybe_tree.failure is not None
-            logger.warning(maybe_tree.failure.message)
-            return code
-        tree = maybe_tree.tree
-        # we won't be doing it like this in production, but for the sake of the example
+    def apply_tree(self, tree: Tree) -> Tree:
+        """Apply the fixes to the AST tree."""
         for node in tree.walk():
             matcher = self._find_matcher(node)
             if matcher is None:
                 continue
             assert isinstance(node, Call)
             matcher.apply(self._from_table, self._index, node)
-        return tree.node.as_string()
+        return tree
 
     def _find_matcher(self, node: NodeNG) -> _TableNameMatcher | None:
         if not isinstance(node, Call):
@@ -476,7 +480,7 @@ def _visit_call_nodes(cls, tree: Tree) -> Iterable[tuple[Call, NodeNG]]:
             yield call_node, query
 
 
-class _SparkSqlPyLinter(_SparkSqlAnalyzer, PythonLinter, Fixer):
+class _SparkSqlPyLinter(_SparkSqlAnalyzer, PythonLinter, PythonFixer):
     """Linter for SparkSQL used within PySpark."""
 
     def __init__(self, sql_linter: SqlLinter, sql_fixer: Fixer | None):
@@ -503,23 +507,18 @@ def lint_tree(self, tree: Tree) -> Iterable[Advice]:
                     code = self.diagnostic_code
                 yield dataclasses.replace(advice.replace_from_node(call_node), code=code)
 
-    def apply(self, code: str) -> str:
+    def apply_tree(self, tree: Tree) -> Tree:
+        """Apply the fixes to the AST tree."""
         if not self._sql_fixer:
-            return code
-        maybe_tree = MaybeTree.from_source_code(code)
-        if maybe_tree.failure:
-            logger.warning(maybe_tree.failure.message)
-            return code
-        assert maybe_tree.tree is not None
-        tree = maybe_tree.tree
+            return tree
         for _call_node, query in self._visit_call_nodes(tree):
             if not isinstance(query, Const) or not isinstance(query.value, str):
                 continue
             # TODO avoid applying same fix multiple times
             # this requires changing 'apply' API in order to check advice fragment location
             new_query = self._sql_fixer.apply(query.value)
             query.value = new_query
-        return tree.node.as_string()
+        return tree
 
 
 class FromTableSqlPyLinter(_SparkSqlPyLinter):