fixed mypy

logic: After processing FILES_MD, the stage is reset to PRS instead of moving to the next repository. This will cause an infinite loop

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

backend/onyx/connectors/github/connector.py

@@ -12,6 +12,7 @@ from typing import cast
 from github import Github
 from github import RateLimitExceededException
 from github import Repository
+from github.ContentFile import ContentFile
 from github.GithubException import GithubException
 from github.Issue import Issue
 from github.NamedUser import NamedUser
@@ -343,6 +344,20 @@ def _convert_issue_to_document(issue: Issue) -> Document:
     )
 
 
+def _convert_file_to_document(file: ContentFile) -> Document:
+    return Document(
+        id=file.html_url,
+        sections=[TextSection(link=file.html_url, text=file.content or "")],
+        source=DocumentSource.GITHUB,
+        semantic_identifier=f"{file.repository.full_name}/{file.path}",
+        metadata={
+            "object_type": "File",
+            "repo": file.repository.full_name if file.repository else "",
+            "path": file.path,
+        },
+    )
+
+
 class SerializedRepository(BaseModel):
     # id is part of the raw_data as well, just pulled out for convenience
     id: int
@@ -359,6 +374,7 @@ class GithubConnectorStage(Enum):
     START = "start"
     PRS = "prs"
     ISSUES = "issues"
+    FILES_MD = "files_md"
 
 
 class GithubConnectorCheckpoint(ConnectorCheckpoint):
@@ -402,12 +418,14 @@ class GithubConnector(CheckpointedConnector[GithubConnectorCheckpoint]):
         state_filter: str = "all",
         include_prs: bool = True,
         include_issues: bool = False,
+        include_files_md: bool = False,
     ) -> None:
         self.repo_owner = repo_owner
         self.repositories = repositories
         self.state_filter = state_filter
         self.include_prs = include_prs
         self.include_issues = include_issues
+        self.include_files_md = include_files_md
         self.github_client: Github | None = None
 
     def load_credentials(self, credentials: dict[str, Any]) -> dict[str, Any] | None:
@@ -504,6 +522,61 @@ class GithubConnector(CheckpointedConnector[GithubConnectorCheckpoint]):
             state=self.state_filter, sort="updated", direction="desc"
         )
 
+    def _files_md_func(self, repo: Repository.Repository) -> list[ContentFile]:
+        github_client = cast(Github, self.github_client)
+
+        def _get_contents_rate_limited(
+            github_client: Github, path: str, attempt_num: int = 0
+        ) -> list[ContentFile]:
+            if attempt_num > _MAX_NUM_RATE_LIMIT_RETRIES:
+                raise RuntimeError(
+                    "Re-tried fetching contents too many times. Something is going wrong with fetching objects from Github"
+                )
+            try:
+                contents = repo.get_contents(path)
+                if isinstance(contents, ContentFile):
+                    contents = [cast(ContentFile, contents)]
+                else:
+                    contents = cast(list[ContentFile], contents)
+                return contents
+            except RateLimitExceededException:
+                _sleep_after_rate_limit_exception(github_client)
+                return _get_contents_rate_limited(github_client, path, attempt_num + 1)
+            except GithubException as e:
+                logger.error(f"Error accessing directory {path}: {e}")
+                return []
+
+        md_files = []
+        contents = _get_contents_rate_limited(github_client, "")
+
+        if isinstance(contents, ContentFile):
+            # if the contents is a single file or directory, we need to wrap it in a list
+            contents = [cast(ContentFile, contents)]
+        else:
+            contents = cast(list[ContentFile], contents)
+
+        while contents:
+            file = contents.pop(0)
+            if file.type == "dir":
+                try:
+                    # if the file is a directory, we need to get the contents of the directory
+                    # and add the contents to the contents list
+                    new_contents = _get_contents_rate_limited(github_client, file.path)
+                    if isinstance(new_contents, ContentFile):
+                        new_contents = [cast(ContentFile, new_contents)]
+                    else:
+                        new_contents = cast(list[ContentFile], new_contents)
+
+                    contents.extend(new_contents)
+                except RateLimitExceededException:
+                    _sleep_after_rate_limit_exception(github_client)
+                    contents.append(file)
+                    continue
+            elif file.type == "file" and file.name.endswith(".md"):
+                md_files.append(file)
+
+        return md_files
+
     def _fetch_from_github(
         self,
         checkpoint: GithubConnectorCheckpoint,
@@ -587,6 +660,8 @@ class GithubConnector(CheckpointedConnector[GithubConnectorCheckpoint]):
             for pr in pr_batch:
                 num_prs += 1
 
+                pr = cast(PullRequest, pr)
+
                 # we iterate backwards in time, so at this point we stop processing prs
                 if (
                     start is not None
@@ -603,7 +678,7 @@ class GithubConnector(CheckpointedConnector[GithubConnectorCheckpoint]):
                 ):
                     continue
                 try:
-                    yield _convert_pr_to_document(cast(PullRequest, pr))
+                    yield _convert_pr_to_document(pr)
                 except Exception as e:
                     error_msg = f"Error converting PR to document: {e}"
                     logger.exception(error_msg)
@@ -659,14 +734,14 @@ class GithubConnector(CheckpointedConnector[GithubConnectorCheckpoint]):
             for issue in issue_batch:
                 num_issues += 1
                 issue = cast(Issue, issue)
-                # we iterate backwards in time, so at this point we stop processing prs
+                # we iterate backwards in time, so at this point we stop processing Issues
                 if (
                     start is not None
                     and issue.updated_at.replace(tzinfo=timezone.utc) < start
                 ):
                     done_with_issues = True
                     break
-                # Skip PRs updated after the end date
+                # Skip Issues updated after the end date
                 if (
                     end is not None
                     and issue.updated_at.replace(tzinfo=timezone.utc) > end
@@ -700,9 +775,44 @@ class GithubConnector(CheckpointedConnector[GithubConnectorCheckpoint]):
 
             # if we went past the start date during the loop or there are no more
             # issues to get, we move on to the next repo
+            checkpoint.stage = GithubConnectorStage.FILES_MD
+            checkpoint.reset()
+
+        checkpoint.stage = GithubConnectorStage.FILES_MD
+
+        if self.include_files_md and checkpoint.stage == GithubConnectorStage.FILES_MD:
+            logger.info(f"Fetching Markdown files for repo: {repo.name}")
+
+            md_files = self._files_md_func(repo)
+
+            checkpoint.curr_page += 1
+            num_files_md = 0
+            for file in md_files:
+                num_files_md += 1
+                file = cast(ContentFile, file)
+                try:
+                    yield _convert_file_to_document(file)
+                except Exception as e:
+                    error_msg = f"Error converting Markdown file to document: {e}"
+                    logger.exception(error_msg)
+                    yield ConnectorFailure(
+                        failed_document=DocumentFailure(
+                            document_id=str(file.html_url),
+                            document_link=file.html_url,
+                        ),
+                        failure_message=error_msg,
+                        exception=e,
+                    )
+
+                    continue
+
+            logger.info(f"Fetched {num_files_md} Markdown files for repo: {repo.name}")
+            logger.info(f"Fetched {num_files_md} Markdown files for repo: {repo.name}")
             checkpoint.stage = GithubConnectorStage.PRS
             checkpoint.reset()
 
+        checkpoint.has_more = len(checkpoint.cached_repo_ids) > 0
+
         checkpoint.has_more = len(checkpoint.cached_repo_ids) > 0
         if checkpoint.cached_repo_ids:
             next_id = checkpoint.cached_repo_ids.pop()

backend/tests/daily/connectors/github/test_github_basic.py

@@ -5,6 +5,7 @@ import pytest
 
 from onyx.configs.constants import DocumentSource
 from onyx.connectors.github.connector import GithubConnector
+from onyx.connectors.models import Document
 from tests.daily.connectors.utils import load_all_docs_from_checkpoint_connector
 
 
@@ -15,6 +16,7 @@ def github_connector() -> GithubConnector:
         repositories="documentation",
         include_prs=True,
         include_issues=True,
+        include_files_md=True,
     )
     connector.load_credentials(
         {
@@ -32,9 +34,16 @@ def test_github_connector_basic(github_connector: GithubConnector) -> None:
     )
     assert len(docs) > 1  # We expect at least one PR and one Issue to exist
 
+    def get_issue_doc(docs: list[Document]) -> Document | None:
+        for doc in docs:
+            if doc.metadata.get("object_type") == "Issue":
+                return doc
+        return None
+
     # Test the first document's structure
     pr_doc = docs[0]
-    issue_doc = docs[-1]
+    issue_doc = get_issue_doc(docs)
+    file_doc = docs[-1]
 
     # Verify basic document properties
     assert pr_doc.source == DocumentSource.GITHUB
@@ -60,6 +69,7 @@ def test_github_connector_basic(github_connector: GithubConnector) -> None:
     assert "created_at" in pr_doc.metadata
 
     # Verify Issue-specific properties
+    assert issue_doc is not None, "Issue document not found"
     assert issue_doc.metadata is not None
     assert issue_doc.metadata.get("object_type") == "Issue"
     assert "id" in issue_doc.metadata
@@ -70,6 +80,12 @@ def test_github_connector_basic(github_connector: GithubConnector) -> None:
     assert "labels" in issue_doc.metadata
     assert "created_at" in issue_doc.metadata
 
+    # Verify File-specific properties
+    assert file_doc.metadata is not None
+    assert file_doc.metadata.get("object_type") == "File"
+    assert "repo" in file_doc.metadata
+    assert "path" in file_doc.metadata
+
     # Verify sections
     assert len(pr_doc.sections) == 1
     section = pr_doc.sections[0]

backend/tests/unit/onyx/connectors/github/test_github_checkpointing.py

@@ -10,6 +10,7 @@ from unittest.mock import patch
 import pytest
 from github import Github
 from github import RateLimitExceededException
+from github.ContentFile import ContentFile
 from github.GithubException import GithubException
 from github.Issue import Issue
 from github.PaginatedList import PaginatedList
@@ -65,6 +66,7 @@ def build_github_connector(
             repositories=repositories,
             include_prs=True,
             include_issues=True,
+            include_files_md=True,
         )
         connector.github_client = mock_github_client
         return connector
@@ -126,6 +128,26 @@ def create_mock_issue() -> Callable[..., MagicMock]:
     return _create_mock_issue
 
 
+@pytest.fixture
+def create_mock_file() -> Callable[..., MagicMock]:
+    def _create_mock_file(
+        name: str = "README.md",
+        html_url: str = "https://github.com/onyx-dot-app/onyx/blob/main/README.md",
+        content: str = "# README",
+        path: str = "README.md",
+        type: str = "file",
+    ) -> MagicMock:
+        mock_file = MagicMock(spec=ContentFile)
+        mock_file.name = name
+        mock_file.html_url = html_url
+        mock_file.content = content
+        mock_file.path = path
+        mock_file.type = type
+        return mock_file
+
+    return _create_mock_file
+
+
 @pytest.fixture
 def create_mock_repo() -> Callable[..., MagicMock]:
     def _create_mock_repo(
@@ -162,6 +184,7 @@ def test_load_from_checkpoint_happy_path(
     create_mock_repo: Callable[..., MagicMock],
     create_mock_pr: Callable[..., MagicMock],
     create_mock_issue: Callable[..., MagicMock],
+    create_mock_file: Callable[..., MagicMock],
 ) -> None:
     """Test loading from checkpoint - happy path"""
     # Set up mocked repo
@@ -170,11 +193,25 @@ def test_load_from_checkpoint_happy_path(
     github_connector.github_client = mock_github_client
     mock_github_client.get_repo.return_value = mock_repo
 
-    # Set up mocked PRs and issues
+    # Set up mocked PRs, issues, and markdown files
     mock_pr1 = create_mock_pr(number=1, title="PR 1")
     mock_pr2 = create_mock_pr(number=2, title="PR 2")
     mock_issue1 = create_mock_issue(number=1, title="Issue 1")
     mock_issue2 = create_mock_issue(number=2, title="Issue 2")
+    mock_file1 = create_mock_file(
+        name="README.md",
+        html_url="https://github.com/test-org/test-repo/blob/main/README.md",
+        content="# README",
+        path="README.md",
+        type="file",
+    )
+    mock_file2 = create_mock_file(
+        name="CONTRIBUTING.md",
+        html_url="https://github.com/test-org/test-repo/blob/main/CONTRIBUTING.md",
+        content="# CONTRIBUTING.md",
+        path="CONTRIBUTING.md",
+        type="file",
+    )
 
     # Mock get_pulls and get_issues methods
     mock_repo.get_pulls.return_value = MagicMock()
@@ -187,6 +224,7 @@ def test_load_from_checkpoint_happy_path(
         [mock_issue1, mock_issue2],
         [],
     ]
+    mock_repo.get_contents.return_value = [mock_file1, mock_file2]
 
     # Mock SerializedRepository.to_Repository to return our mock repo
     with patch.object(SerializedRepository, "to_Repository", return_value=mock_repo):
@@ -225,10 +263,23 @@ def test_load_from_checkpoint_happy_path(
         )
         assert second_batch.next_checkpoint.has_more
 
-        # Check third batch (finished checkpoint)
+        # Check third batch (Markdown files)
         third_batch = outputs[3]
-        assert len(third_batch.items) == 0
-        assert third_batch.next_checkpoint.has_more is False
+        assert len(third_batch.items) == 2
+        assert isinstance(third_batch.items[0], Document)
+        assert (
+            third_batch.items[0].id
+            == "https://github.com/test-org/test-repo/blob/main/README.md"
+        )
+        assert isinstance(third_batch.items[1], Document)
+        assert (
+            third_batch.items[1].id
+            == "https://github.com/test-org/test-repo/blob/main/CONTRIBUTING.md"
+        )
+
+        # Check final batch (finished checkpoint)
+        final_batch = outputs[-1]
+        assert final_batch.next_checkpoint.has_more is False
 
 
 def test_load_from_checkpoint_with_rate_limit(
@@ -294,11 +345,12 @@ def test_load_from_checkpoint_with_empty_repo(
     github_connector.github_client = mock_github_client
     mock_github_client.get_repo.return_value = mock_repo
 
-    # Mock get_pulls and get_issues to return empty lists
+    # Mock get_pulls, get_issues, and get_contents to return empty lists
     mock_repo.get_pulls.return_value = MagicMock()
     mock_repo.get_pulls.return_value.get_page.return_value = []
     mock_repo.get_issues.return_value = MagicMock()
     mock_repo.get_issues.return_value.get_page.return_value = []
+    mock_repo.get_contents.return_value = []
 
     # Mock SerializedRepository.to_Repository to return our mock repo
     with patch.object(SerializedRepository, "to_Repository", return_value=mock_repo):
@@ -309,8 +361,8 @@ def test_load_from_checkpoint_with_empty_repo(
         )
 
         # Check that we got no documents
-        assert len(outputs) == 2
-        assert len(outputs[-1].items) == 0
+        assert len(outputs) == 3
+        assert len(outputs[1].items) == 0
         assert not outputs[-1].next_checkpoint.has_more
 
 
@@ -886,7 +938,7 @@ def test_load_from_checkpoint_cursor_pagination_completion(
     assert cp4.cached_repo is not None
     assert cp4.cached_repo.id == mock_repo1.id  # Last processed repo
     assert (
-        cp4.stage == GithubConnectorStage.PRS
+        cp4.stage == GithubConnectorStage.FILES_MD
     )  # Reset for a hypothetical next run/repo
     assert cp4.curr_page == 0
     assert cp4.num_retrieved == 0

web/src/lib/connectors/connectors.tsx

@@ -242,6 +242,14 @@ export const connectorConfigs: Record<
         description: "Index issues from repositories",
         optional: true,
       },
+      {
+        type: "checkbox",
+        query: "Include Markdown files?",
+        label: "Include Markdown files?",
+        name: "include_files_md",
+        description: "Index Markdown files from repositories",
+        optional: true,
+      },
     ],
     advanced_values: [],
   },
@@ -1492,6 +1500,7 @@ export interface GithubConfig {
   repositories: string; // Comma-separated list of repository names
   include_prs: boolean;
   include_issues: boolean;
+  include_files_md?: boolean;
 }
 
 export interface GitlabConfig {