Add Deeplinks to Improve Context for Document Retrieval (#1206)

## Overview
Show deep link URI and raw document context to provide deeper, richer
context to Khoj. This should allow it better combine semantic search
with other new document retrieval tools like line range based file
viewer and regex tools added in #1205

## Details
- Attach line number based deeplinks to each indexed document entry
Document URI follows URL fragment based schema of form
`file:///path/to/file.txt#line=123`
- Show raw indexed document entries with deep links to LLM when it uses
the semantic search tool
- Reduce structural changes to raw org-mode entries for easier deep
linking.

src/khoj/database/models/__init__.py

@@ -23,6 +23,7 @@ logger = logging.getLogger(__name__)
 class Context(PydanticBaseModel):
     compiled: str
     file: str
+    uri: str
     query: Optional[str] = None
 
 

src/khoj/processor/content/markdown/markdown_to_entries.py

@@ -54,13 +54,13 @@ class MarkdownToEntries(TextToEntries):
     def extract_markdown_entries(markdown_files: Dict[str, str], max_tokens=256) -> Tuple[Dict[str, str], List[Entry]]:
         "Extract entries by heading from specified Markdown files"
         entries: List[str] = []
-        entry_to_file_map: List[Tuple[str, str]] = []
+        entry_to_file_map: List[Tuple[str, str, int]] = []
         file_to_text_map: Dict[str, str] = dict()
         for markdown_file in markdown_files:
             try:
                 markdown_content = markdown_files[markdown_file]
                 entries, entry_to_file_map = MarkdownToEntries.process_single_markdown_file(
-                    markdown_content, markdown_file, entries, entry_to_file_map, max_tokens
+                    markdown_content, markdown_file, entries, entry_to_file_map, max_tokens, start_line=1
                 )
                 file_to_text_map[markdown_file] = markdown_content
             except Exception as e:
@@ -68,17 +68,18 @@ class MarkdownToEntries(TextToEntries):
                     f"Unable to process file: {markdown_file}. This file will not be indexed.\n{e}", exc_info=True
                 )
 
-        return file_to_text_map, MarkdownToEntries.convert_markdown_entries_to_maps(entries, dict(entry_to_file_map))
+        return file_to_text_map, MarkdownToEntries.convert_markdown_entries_to_maps(entries, entry_to_file_map)
 
     @staticmethod
     def process_single_markdown_file(
         markdown_content: str,
         markdown_file: str,
         entries: List[str],
-        entry_to_file_map: List[Tuple[str, str]],
+        entry_to_file_map: List[Tuple[str, str, int]],
         max_tokens=256,
         ancestry: Dict[int, str] = {},
-    ) -> Tuple[List[str], List[Tuple[str, str]]]:
+        start_line: int = 1,
+    ) -> Tuple[List[str], List[Tuple[str, str, int]]]:
         # Prepend the markdown section's heading ancestry
         ancestry_string = "\n".join([f"{'#' * key} {ancestry[key]}" for key in sorted(ancestry.keys())])
         markdown_content_with_ancestry = f"{ancestry_string}{markdown_content}"
@@ -87,7 +88,9 @@ class MarkdownToEntries(TextToEntries):
         if len(TextToEntries.tokenizer(markdown_content_with_ancestry)) <= max_tokens or not re.search(
             rf"^#{{{len(ancestry)+1},}}\s", markdown_content, flags=re.MULTILINE
         ):
-            entry_to_file_map += [(markdown_content_with_ancestry, markdown_file)]
+            # Create entry with line number information
+            entry_with_line_info = (markdown_content_with_ancestry, markdown_file, start_line)
+            entry_to_file_map += [entry_with_line_info]
             entries.extend([markdown_content_with_ancestry])
             return entries, entry_to_file_map
 
@@ -98,22 +101,32 @@ class MarkdownToEntries(TextToEntries):
             next_heading_level += 1
             sections = re.split(rf"(\n|^)(?=[#]{{{next_heading_level}}} .+\n?)", markdown_content, flags=re.MULTILINE)
 
+        # Recurse down each non-empty section after parsing its body, heading and ancestry
+        current_line_offset = 0
         for section in sections:
+            num_lines_in_section = section.count("\n")
             # Skip empty sections
             if section.strip() == "":
+                current_line_offset += num_lines_in_section
                 continue
 
+            section_start_line_in_file = start_line + current_line_offset
+
             # Extract the section body and (when present) the heading
             current_ancestry = ancestry.copy()
             first_line = [line for line in section.split("\n") if line.strip() != ""][0]
             if re.search(rf"^#{{{next_heading_level}}} ", first_line):
                 # Extract the section body without the heading
-                current_section_body = "\n".join(section.split(first_line)[1:])
+                current_section_heading, current_section_body = section.split(first_line, 1)
+                current_section_body_offset = current_section_heading.count("\n")
                 # Parse the section heading into current section ancestry
                 current_section_title = first_line[next_heading_level:].strip()
                 current_ancestry[next_heading_level] = current_section_title
+                # Line number should point to the heading itself
+                recursive_start_line = section_start_line_in_file + current_section_body_offset
             else:
                 current_section_body = section
+                recursive_start_line = section_start_line_in_file
 
             # Recurse down children of the current entry
             MarkdownToEntries.process_single_markdown_file(
@@ -123,23 +136,38 @@ class MarkdownToEntries(TextToEntries):
                 entry_to_file_map,
                 max_tokens,
                 current_ancestry,
+                start_line=recursive_start_line,
             )
+            current_line_offset += num_lines_in_section
 
         return entries, entry_to_file_map
 
     @staticmethod
-    def convert_markdown_entries_to_maps(parsed_entries: List[str], entry_to_file_map: Dict[str, str]) -> List[Entry]:
+    def convert_markdown_entries_to_maps(
+        parsed_entries: List[str], entry_to_file_map: List[Tuple[str, str, int]]
+    ) -> List[Entry]:
         "Convert each Markdown entries into a dictionary"
         entries: List[Entry] = []
+
+        # Create a mapping from parsed entry to file info
+        entry_map: Dict[str, Tuple[str, int]] = {}
+        for entry_info in entry_to_file_map:
+            entry_content, raw_filename, start_line = entry_info
+            entry_map[entry_content] = (raw_filename, start_line)
+
         for parsed_entry in parsed_entries:
-            raw_filename = entry_to_file_map[parsed_entry]
+            raw_filename, start_line = entry_map[parsed_entry]
+            calculated_line = start_line if start_line > 0 else 1
 
             # Check if raw_filename is a URL. If so, save it as is. If not, convert it to a Path.
             if type(raw_filename) == str and re.search(r"^https?://", raw_filename):
                 # Escape the URL to avoid issues with special characters
                 entry_filename = urllib3.util.parse_url(raw_filename).url
+                uri = entry_filename
             else:
                 entry_filename = raw_filename
+                # Create URI with line number
+                uri = f"file://{entry_filename}#line={calculated_line}"
 
             heading = parsed_entry.splitlines()[0] if re.search(r"^#+\s", parsed_entry) else ""
             # Append base filename to compiled entry for context to model
@@ -152,6 +180,7 @@ class MarkdownToEntries(TextToEntries):
                     raw=parsed_entry,
                     heading=f"{prefix}{heading}",
                     file=entry_filename,
+                    uri=uri,
                 )
             )
 

src/khoj/processor/content/org_mode/org_to_entries.py

@@ -87,6 +87,7 @@ class OrgToEntries(TextToEntries):
         entry_to_file_map: List[Tuple[Orgnode, str]],
         max_tokens=256,
         ancestry: Dict[int, str] = {},
+        start_line: int = 1,
     ) -> Tuple[List[List[Orgnode]], List[Tuple[Orgnode, str]]]:
         """Parse org_content from org_file into OrgNode entries
 
@@ -104,7 +105,9 @@ class OrgToEntries(TextToEntries):
         if len(TextToEntries.tokenizer(org_content_with_ancestry)) <= max_tokens or not re.search(
             rf"^\*{{{len(ancestry)+1},}}\s", org_content, re.MULTILINE
         ):
-            orgnode_content_with_ancestry = orgnode.makelist(org_content_with_ancestry, org_file)
+            orgnode_content_with_ancestry = orgnode.makelist(
+                org_content_with_ancestry, org_file, start_line=start_line, ancestry_lines=len(ancestry)
+            )
             entry_to_file_map += zip(orgnode_content_with_ancestry, [org_file] * len(orgnode_content_with_ancestry))
             entries.extend([orgnode_content_with_ancestry])
             return entries, entry_to_file_map
@@ -125,24 +128,32 @@ class OrgToEntries(TextToEntries):
             return entries, entry_to_file_map
 
         # Recurse down each non-empty section after parsing its body, heading and ancestry
+        current_line_offset = 0
         for section in sections:
+            num_lines_in_section = section.count("\n")
             # Skip empty sections
             if section.strip() == "":
+                current_line_offset += num_lines_in_section
                 continue
 
+            section_start_line_in_file = start_line + current_line_offset
+
             # Extract the section body and (when present) the heading
             current_ancestry = ancestry.copy()
             first_non_empty_line = [line for line in section.split("\n") if line.strip() != ""][0]
             # If first non-empty line is a heading with expected heading level
             if re.search(rf"^\*{{{next_heading_level}}}\s", first_non_empty_line):
                 # Extract the section body without the heading
-                current_section_body = "\n".join(section.split(first_non_empty_line, 1)[1:])
+                current_section_heading, current_section_body = section.split(first_non_empty_line, 1)
+                current_section_body_offset = current_section_heading.count("\n")
                 # Parse the section heading into current section ancestry
                 current_section_title = first_non_empty_line[next_heading_level:].strip()
                 current_ancestry[next_heading_level] = current_section_title
+                recursive_start_line = section_start_line_in_file + current_section_body_offset
             # Else process the section as just body text
             else:
                 current_section_body = section
+                recursive_start_line = section_start_line_in_file
 
             # Recurse down children of the current entry
             OrgToEntries.process_single_org_file(
@@ -152,7 +163,9 @@ class OrgToEntries(TextToEntries):
                 entry_to_file_map,
                 max_tokens,
                 current_ancestry,
+                start_line=recursive_start_line,
             )
+            current_line_offset += num_lines_in_section
 
         return entries, entry_to_file_map
 
@@ -207,6 +220,8 @@ class OrgToEntries(TextToEntries):
                 if parsed_entry.hasBody:
                     compiled += f"\n {parsed_entry.body}"
 
+                uri = parsed_entry.properties.pop("LINE", None)
+
                 # Add the sub-entry contents to the entry
                 entry_compiled += compiled
                 entry_raw += f"{parsed_entry}"
@@ -220,6 +235,7 @@ class OrgToEntries(TextToEntries):
                         raw=entry_raw,
                         heading=entry_heading,
                         file=entry_to_file_map[parsed_entry],
+                        uri=uri,
                     )
                 )
 

src/khoj/processor/content/org_mode/orgnode.py

@@ -58,7 +58,7 @@ def makelist_with_filepath(filename):
     return makelist(f, filename)
 
 
-def makelist(file, filename) -> List["Orgnode"]:
+def makelist(file, filename, start_line: int = 1, ancestry_lines: int = 0) -> List["Orgnode"]:
     """
     Read an org-mode file and return a list of Orgnode objects
     created from this file.
@@ -66,7 +66,7 @@ def makelist(file, filename) -> List["Orgnode"]:
     ctr = 0
 
     if type(file) == str:
-        f = file.split("\n")
+        f = file.splitlines()
     else:
         f = file
 
@@ -114,14 +114,23 @@ def makelist(file, filename) -> List["Orgnode"]:
                     logbook = list()
                 thisNode.properties = property_map
                 nodelist.append(thisNode)
-            property_map = {"LINE": f"file:{normalize_filename(filename)}::{ctr}"}
+            # Account for ancestry lines that were prepended when calculating line numbers
+            if ancestry_lines > 0:
+                calculated_line = start_line + ctr - 1 - ancestry_lines
+                if calculated_line <= 0:
+                    calculated_line = 1  # Fallback to line 1 if calculation results in invalid line number
+            else:
+                calculated_line = start_line + ctr - 1
+                if calculated_line <= 0:
+                    calculated_line = ctr  # Use the original behavior if start_line calculation fails
+            property_map = {"LINE": f"file://{normalize_filename(filename)}#line={calculated_line}"}
             previous_level = level
             previous_heading: str = heading
             level = heading_search.group(1)
             heading = heading_search.group(2)
             bodytext = ""
             tags = list()  # set of all tags in headline
-            tag_search = re.search(r"(.*?)\s*:([a-zA-Z0-9].*?):$", heading)
+            tag_search = re.search(r"(.*?)\s+:([a-zA-Z0-9@_].*?):\s*$", heading)
             if tag_search:
                 heading = tag_search.group(1)
                 parsedtags = tag_search.group(2)
@@ -260,14 +269,6 @@ def makelist(file, filename) -> List["Orgnode"]:
         # Prefix filepath/title to ancestors
         n.ancestors = [file_title] + n.ancestors
 
-        # Set SOURCE property to a file+heading based org-mode link to the entry
-        if n.level == 0:
-            n.properties["LINE"] = f"file:{normalize_filename(filename)}::0"
-            n.properties["SOURCE"] = f"[[file:{normalize_filename(filename)}]]"
-        else:
-            escaped_heading = n.heading.replace("[", "\\[").replace("]", "\\]")
-            n.properties["SOURCE"] = f"[[file:{normalize_filename(filename)}::*{escaped_heading}]]"
-
     return nodelist
 
 
@@ -520,10 +521,11 @@ class Orgnode(object):
             n = n + "\n"
 
         # Output Property Drawer
-        n = n + indent + ":PROPERTIES:\n"
-        for key, value in self._properties.items():
-            n = n + indent + f":{key}: {value}\n"
-        n = n + indent + ":END:\n"
+        if self._properties:
+            n = n + indent + ":PROPERTIES:\n"
+            for key, value in self._properties.items():
+                n = n + indent + f":{key}: {value}\n"
+            n = n + indent + ":END:\n"
 
         # Output Body
         if self.hasBody:

src/khoj/processor/content/text_to_entries.py

@@ -81,8 +81,35 @@ class TextToEntries(ABC):
             chunked_entry_chunks = text_splitter.split_text(entry.compiled)
             corpus_id = uuid.uuid4()
 
+            line_start = None
+            last_offset = 0
+            if entry.uri and entry.uri.startswith("file://"):
+                if "#line=" in entry.uri:
+                    line_start = int(entry.uri.split("#line=", 1)[-1].split("&", 1)[0])
+                else:
+                    line_start = 0
+
             # Create heading prefixed entry from each chunk
             for chunk_index, compiled_entry_chunk in enumerate(chunked_entry_chunks):
+                # set line start in uri of chunked entries
+                entry_uri = entry.uri
+                if line_start is not None:
+                    # Find the chunk in the raw text to get an accurate line number.
+                    # Search for the unmodified chunk from the last offset.
+                    searchable_chunk = compiled_entry_chunk.strip()
+                    if searchable_chunk:
+                        chunk_start_pos_in_raw = entry.raw.find(searchable_chunk, last_offset)
+                        if chunk_start_pos_in_raw != -1:
+                            # Found the chunk. Calculate its line offset from the start of the raw text.
+                            line_offset_in_raw = entry.raw[:chunk_start_pos_in_raw].count("\n")
+                            new_line_num = line_start + line_offset_in_raw
+                            entry_uri = re.sub(r"#line=\d+", f"#line={new_line_num}", entry.uri)
+                            # Update search position for the next chunk to start after the current one.
+                            last_offset = chunk_start_pos_in_raw + len(searchable_chunk)
+                        else:
+                            # Chunk not found in raw text, likely from a heading. Use original line_start.
+                            entry_uri = re.sub(r"#line=\d+", f"#line={line_start}", entry.uri)
+
                 # Prepend heading to all other chunks, the first chunk already has heading from original entry
                 if chunk_index > 0 and entry.heading:
                     # Snip heading to avoid crossing max_tokens limit
@@ -99,6 +126,7 @@ class TextToEntries(ABC):
                 entry.raw = compiled_entry_chunk if raw_is_compiled else TextToEntries.clean_field(entry.raw)
                 entry.heading = TextToEntries.clean_field(entry.heading)
                 entry.file = TextToEntries.clean_field(entry.file)
+                entry_uri = TextToEntries.clean_field(entry_uri)
 
                 chunked_entries.append(
                     Entry(
@@ -107,6 +135,7 @@ class TextToEntries(ABC):
                         heading=entry.heading,
                         file=entry.file,
                         corpus_id=corpus_id,
+                        uri=entry_uri,
                     )
                 )
 
@@ -192,6 +221,7 @@ class TextToEntries(ABC):
                             file_type=file_type,
                             hashed_value=entry_hash,
                             corpus_id=entry.corpus_id,
+                            url=entry.uri,
                             search_model=model,
                             file_object=file_object,
                         )

src/khoj/processor/conversation/utils.py

@@ -646,7 +646,7 @@ def generate_chatml_messages_with_context(
 
         if not is_none_or_empty(chat.context):
             references = "\n\n".join(
-                {f"# File: {item.file}\n## {item.compiled}\n" for item in chat.context or [] if isinstance(item, dict)}
+                {f"# URI: {item.uri}\n## {item.compiled}\n" for item in chat.context or [] if isinstance(item, dict)}
             )
             message_context += [{"type": "text", "text": f"{prompts.notes_conversation.format(references=references)}"}]
 

src/khoj/routers/helpers.py

@@ -1263,8 +1263,9 @@ async def search_documents(
         compiled_references = [
             {
                 "query": item.additional["query"],
-                "compiled": item.additional["compiled"],
+                "compiled": item["entry"],
                 "file": item.additional["file"],
+                "uri": item.additional["uri"],
             }
             for item in search_results
         ]
@@ -2867,6 +2868,7 @@ async def view_file_content(
             {
                 "query": query,
                 "file": path,
+                "uri": path,
                 "compiled": filtered_text,
             }
         ]
@@ -2878,7 +2880,7 @@ async def view_file_content(
         logger.error(error_msg, exc_info=True)
 
         # Return an error result in the expected format
-        yield [{"query": query, "file": path, "compiled": error_msg}]
+        yield [{"query": query, "file": path, "uri": path, "compiled": error_msg}]
 
 
 async def grep_files(
@@ -2982,7 +2984,7 @@ async def grep_files(
             max_results,
         )
         if not line_matches:
-            yield {"query": query, "file": path_prefix, "compiled": "No matches found."}
+            yield {"query": query, "file": path_prefix, "uri": path_prefix, "compiled": "No matches found."}
             return
 
         # Truncate matched lines list if too long
@@ -2991,7 +2993,7 @@ async def grep_files(
                 f"... {len(line_matches) - max_results} more results found. Use stricter regex or path to narrow down results."
             ]
 
-        yield {"query": query, "file": path_prefix or "", "compiled": "\n".join(line_matches)}
+        yield {"query": query, "file": path_prefix, "uri": path_prefix, "compiled": "\n".join(line_matches)}
 
     except Exception as e:
         error_msg = f"Error using grep files tool: {str(e)}"
@@ -3000,6 +3002,7 @@ async def grep_files(
             {
                 "query": _generate_query(0, 0, path_prefix or "", regex_pattern, lines_before, lines_after),
                 "file": path_prefix,
+                "uri": path_prefix,
                 "compiled": error_msg,
             }
         ]
@@ -3032,7 +3035,7 @@ async def list_files(
             file_objects = await FileObjectAdapters.aget_file_objects_by_path_prefix(user, path)
 
         if not file_objects:
-            yield {"query": _generate_query(0, path, pattern), "file": path, "compiled": "No files found."}
+            yield {"query": _generate_query(0, path, pattern), "file": path, "uri": path, "compiled": "No files found."}
             return
 
         # Extract file names from file objects
@@ -3047,7 +3050,7 @@ async def list_files(
 
         query = _generate_query(len(files), path, pattern)
         if not files:
-            yield {"query": query, "file": path, "compiled": "No files found."}
+            yield {"query": query, "file": path, "uri": path, "compiled": "No files found."}
             return
 
         # Truncate the list if it's too long
@@ -3057,9 +3060,9 @@ async def list_files(
                 f"... {len(files) - max_files} more files found. Use glob pattern to narrow down results."
             ]
 
-        yield {"query": query, "file": path, "compiled": "\n- ".join(files)}
+        yield {"query": query, "file": path, "uri": path, "compiled": "\n- ".join(files)}
 
     except Exception as e:
         error_msg = f"Error listing files in {path}: {str(e)}"
         logger.error(error_msg, exc_info=True)
-        yield {"query": query, "file": path, "compiled": error_msg}
+        yield {"query": query, "file": path, "uri": path, "compiled": error_msg}

src/khoj/search_type/text_search.py

@@ -157,6 +157,7 @@ def collate_results(hits, dedupe=True):
                     "additional": {
                         "source": hit.file_source,
                         "file": hit.file_path,
+                        "uri": hit.url,
                         "compiled": hit.compiled,
                         "heading": hit.heading,
                     },
@@ -180,6 +181,7 @@ def deduplicated_search_responses(hits: List[SearchResponse]):
                     "additional": {
                         "source": hit.additional["source"],
                         "file": hit.additional["file"],
+                        "uri": hit.additional["uri"],
                         "query": hit.additional["query"],
                         "compiled": hit.additional["compiled"],
                         "heading": hit.additional["heading"],

src/khoj/utils/rawconfig.py

@@ -176,6 +176,7 @@ class Entry:
     compiled: str
     heading: Optional[str]
     file: Optional[str]
+    uri: Optional[str] = None
     corpus_id: str
 
     def __init__(
@@ -184,6 +185,7 @@ class Entry:
         compiled: str = None,
         heading: Optional[str] = None,
         file: Optional[str] = None,
+        uri: Optional[str] = None,
         corpus_id: uuid.UUID = None,
     ):
         self.raw = raw
@@ -191,6 +193,14 @@ class Entry:
         self.heading = heading
         self.file = file
         self.corpus_id = str(corpus_id)
+        if uri:
+            self.uri = uri
+        elif file and (file.startswith("http") or file.startswith("file://")):
+            self.uri = file
+        elif file:
+            self.uri = f"file://{file}"
+        else:
+            self.uri = None
 
     def to_json(self) -> str:
         return json.dumps(self.__dict__, ensure_ascii=False)
@@ -206,4 +216,5 @@ class Entry:
             file=dictionary.get("file", None),
             heading=dictionary.get("heading", None),
             corpus_id=dictionary.get("corpus_id", None),
+            uri=dictionary.get("uri", None),
         )

tests/data/markdown/main_readme.md

@@ -0,0 +1,39 @@
+# Main Readme
+> Allow natural language search, chat with your documents using transformer based models
+
+This is a test markdown file with multiple, nested child entries.
+
+## Dependencies
+
+- Python3
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links)
+
+## Installation
+
+```bash
+pip install khoj
+```
+
+## Run
+  Load ML model, generate embeddings and expose API to query specified org-mode files
+
+  ```shell
+  python3 main.py --input-files ~/Notes/Schedule.org ~/Notes/Incoming.org --verbose
+  ```
+
+## Use
+
+### **Khoj via API**
+- Query: `GET` [http://localhost:42110/api/search?q="What is the meaning of life"](http://localhost:42110/api/search?q=%22what%20is%20the%20meaning%20of%20life%22)
+- Update Index: `GET` [http://localhost:42110/api/update](http://localhost:42110/api/update)
+- [Khoj API Docs](http://localhost:42110/docs)
+
+### *Khoj via Web*
+
+- Open browser to http://localhost:42110
+- Enter query in search box
+
+## Acknowledgments
+
+- [MiniLM Model](https://huggingface.co/sentence-transformers/multi-qa-MiniLM-L6-cos-v1) for Asymmetric Text Search. See (SBert Documentation)[https://www.sbert.net/examples/applications/retrieve_rerank/README.html]
+- [OpenAI CLIP Model](https://github.com/openai/CLIP) for Image Search. See [SBert Documentation](https://www.sbert.net/examples/applications/image-search/README.html)

tests/data/org/main_readme.org

@@ -3,7 +3,7 @@
 
   All data is processed locally. User can interface with khoj app via [[./interface/emacs/khoj.el][Emacs]], API or Commandline
 
-** Dependencies
+** Dependencies [[id:123-421-121-12]]  :TAG1:@TAG1_1:
    - Python3
    - [[https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links][Miniconda]]
 
@@ -22,7 +22,7 @@
    #+end_src
 
 ** Use
-*** *Khoj via Emacs*
+*** *Khoj via Emacs*  [[https://khoj.dev][link to khoj website]]  :@EMACS:CLIENT_1:KHOJ:
      - [[https://github.com/khoj-ai/khoj/tree/master/interface/emacs#installation][Install]] [[./interface/emacs/khoj.el][khoj.el]]
      - Run ~M-x khoj <user-query>~ or Call ~C-c C-s~
 

tests/test_markdown_to_entries.py

@@ -1,4 +1,5 @@
 import os
+import re
 from pathlib import Path
 
 from khoj.processor.content.markdown.markdown_to_entries import MarkdownToEntries
@@ -248,6 +249,58 @@ def test_get_markdown_files(tmp_path):
     assert set(extracted_org_files.keys()) == expected_files
 
 
+def test_line_number_tracking_in_recursive_split():
+    "Ensure line numbers in URIs are correct after recursive splitting by checking against the actual file."
+    # Arrange
+    markdown_file_path = os.path.abspath("tests/data/markdown/main_readme.md")
+
+    with open(markdown_file_path, "r") as f:
+        markdown_content = f.read()
+    lines = markdown_content.splitlines()
+    data = {markdown_file_path: markdown_content}
+
+    # Act
+    # Using a small max_tokens to force recursive splitting
+    _, entries = MarkdownToEntries.extract_markdown_entries(markdown_files=data, max_tokens=10)
+
+    # Assert
+    assert len(entries) > 0, "No entries were extracted."
+
+    for entry in entries:
+        # Extract file path and line number from the entry URI
+        # for files uri is expected in format: file:///path/to/file.md#line=5
+        match = re.search(r"file://(.*?)#line=(\d+)", entry.uri)
+        filepath_from_uri = match.group(1)
+        line_number_from_uri = int(match.group(2))
+
+        # line_number is 1-based, list index is 0-based
+        line_in_file = clean(lines[line_number_from_uri - 1])
+        next_line_in_file = clean(lines[line_number_from_uri]) if line_number_from_uri < len(lines) else ""
+
+        # Remove ancestor heading lines inserted during post-processing
+        first_entry_line = ""
+        for line in entry.raw.splitlines():
+            if line.startswith("#"):
+                first_entry_line = line
+            else:
+                break  # Stop at the first non-heading line
+        # Remove heading prefix from entry.compiled as level changed during post-processing
+        cleaned_first_entry_line = first_entry_line.strip()
+        # Remove multiple consecutive spaces
+        cleaned_first_entry_line = clean(cleaned_first_entry_line)
+
+        assert entry.uri is not None, f"Entry '{entry}' has a None URI."
+        assert match is not None, f"URI format is incorrect: {entry.uri}"
+        assert (
+            filepath_from_uri == markdown_file_path
+        ), f"File path in URI '{filepath_from_uri}' does not match expected '{markdown_file_path}'"
+
+        # Ensure the first non-heading line in the compiled entry matches the line in the file
+        assert (
+            cleaned_first_entry_line in line_in_file.strip() or cleaned_first_entry_line in next_line_in_file.strip()
+        ), f"First non-heading line '{cleaned_first_entry_line}' in {entry.raw} does not match line {line_number_from_uri} in file: '{line_in_file}' or next line '{next_line_in_file}'"
+
+
 # Helper Functions
 def create_file(tmp_path: Path, entry=None, filename="test.md"):
     markdown_file = tmp_path / filename
@@ -255,3 +308,8 @@ def create_file(tmp_path: Path, entry=None, filename="test.md"):
     if entry:
         markdown_file.write_text(entry)
     return markdown_file
+
+
+def clean(text):
+    "Normalize spaces in text for easier comparison."
+    return re.sub(r"\s+", " ", text)

tests/test_org_to_entries.py

@@ -147,12 +147,10 @@ body line 1.1
     # Extract Entries from specified Org files
     extracted_entries = OrgToEntries.extract_org_entries(org_files=data, max_tokens=12)
     assert len(extracted_entries) == 2
-    for entry in extracted_entries[1]:
-        entry.raw = clean(entry.raw)
 
     # Assert
     assert len(extracted_entries[1]) == 1
-    assert entry.raw == expected_entry
+    assert extracted_entries[1][-1].raw == expected_entry
 
 
 def test_parse_org_entry_with_children_as_single_entry_if_small(tmp_path):
@@ -388,8 +386,6 @@ def test_extract_entries_with_different_level_headings(tmp_path):
     # Extract Entries from specified Org files
     entries = OrgToEntries.extract_org_entries(org_files=data, index_heading_entries=True, max_tokens=3)
     assert len(entries) == 2
-    for entry in entries[1]:
-        entry.raw = clean(f"{entry.raw}")
 
     # Assert
     assert len(entries[1]) == 2
@@ -397,6 +393,60 @@ def test_extract_entries_with_different_level_headings(tmp_path):
     assert entries[1][1].raw == "* Heading 2\n"
 
 
+def test_line_number_tracking_in_recursive_split():
+    "Ensure line numbers in URIs are correct after recursive splitting by checking against the actual file."
+    # Arrange
+    org_file_path = os.path.abspath("tests/data/org/main_readme.org")
+
+    with open(org_file_path, "r") as f:
+        org_content = f.read()
+    lines = org_content.splitlines()
+    data = {org_file_path: org_content}
+
+    # Act
+    # Using a small max_tokens to force recursive splitting
+    _, entries = OrgToEntries.extract_org_entries(org_files=data, max_tokens=10, index_heading_entries=True)
+
+    # Assert
+    assert len(entries) > 0, "No entries were extracted."
+
+    for entry in entries:
+        # Extract file path and line number from the entry URI
+        # for files uri is expected in format: file:///path/to/file.org#line=5
+        match = re.search(r"file://(.*?)#line=(\d+)", entry.uri)
+        if not match:
+            continue
+        filepath_from_uri = match.group(1)
+        line_number_from_uri = int(match.group(2))
+
+        # line_number is 1-based, list index is 0-based
+        line_in_file = clean(lines[line_number_from_uri - 1])
+        next_line_in_file = clean(lines[line_number_from_uri]) if line_number_from_uri < len(lines) else ""
+
+        # Remove ancestor heading lines inserted during post-processing
+        first_entry_line = ""
+        for line in entry.raw.splitlines():
+            if line.startswith("*"):
+                first_entry_line = line
+            else:
+                break  # Stop at the first non-heading line
+        # Remove heading prefix from entry.compiled as level changed during post-processing
+        cleaned_first_entry_line = first_entry_line.strip()
+        # Remove multiple consecutive spaces
+        cleaned_first_entry_line = clean(cleaned_first_entry_line)
+
+        assert entry.uri is not None, f"Entry '{entry}' has a None URI."
+        assert match is not None, f"URI format is incorrect: {entry.uri}"
+        assert (
+            filepath_from_uri == org_file_path
+        ), f"File path in URI '{filepath_from_uri}' does not match expected '{org_file_path}'"
+
+        # Ensure the first non-heading line in the compiled entry matches the line in the file
+        assert (
+            cleaned_first_entry_line in line_in_file.strip() or cleaned_first_entry_line in next_line_in_file.strip()
+        ), f"First non-heading line '{cleaned_first_entry_line}' in {entry.raw} does not match line {line_number_from_uri} in file: '{line_in_file}' or next line '{next_line_in_file}'"
+
+
 # Helper Functions
 def create_file(tmp_path, entry=None, filename="test.org"):
     org_file = tmp_path / filename
@@ -406,6 +456,6 @@ def create_file(tmp_path, entry=None, filename="test.org"):
     return org_file
 
 
-def clean(entry):
-    "Remove properties from entry for easier comparison."
-    return re.sub(r"\n:PROPERTIES:(.*?):END:", "", entry, flags=re.DOTALL)
+def clean(text):
+    "Normalize spaces in text for easier comparison."
+    return re.sub(r"\s+", " ", text)

tests/test_orgnode.py

@@ -100,9 +100,8 @@ def test_render_entry_with_property_drawer_and_empty_body(tmp_path):
 
     expected_entry = f"""*** [#A] Heading1                                            :tag1:
 :PROPERTIES:
-:LINE: file:{orgfile}::2
+:LINE: file://{orgfile}#line=2
 :ID: id:111-111-111-1111-1111
-:SOURCE: [[file:{orgfile}::*Heading1]]
 :END:
 """
 
@@ -133,37 +132,12 @@ Body Line 2
 
     # Assert
     # SOURCE link rendered with Heading
-    assert f":SOURCE: [[file:{orgfile}::*{entries[0].heading}]]" in f"{entries[0]}"
     # ID link rendered with ID
     assert f":ID: id:123-456-789-4234-1231" in f"{entries[0]}"
     # LINE link rendered with line number
-    assert f":LINE: file:{orgfile}::2" in f"{entries[0]}"
-
-
-# ----------------------------------------------------------------------------------------------------
-def test_source_link_to_entry_escaped_for_rendering(tmp_path):
-    "Test SOURCE link renders with square brackets in filename, heading escaped for org-mode rendering"
-    # Arrange
-    entry = f"""
-*** [#A] Heading[1]   :tag1:
-:PROPERTIES:
-:ID: 123-456-789-4234-1231
-:END:
-Body Line 1"""
-    orgfile = create_file(tmp_path, entry, filename="test[1].org")
-
-    # Act
-    entries = orgnode.makelist_with_filepath(orgfile)
-
-    # Assert
-    assert len(entries) == 1
-    # parsed heading from entry
-    assert entries[0].heading == "Heading[1]"
-    # track ancestors of entry
-    assert entries[0].ancestors == [f"{orgfile}"]
-    # ensure SOURCE link has square brackets in filename, heading escaped in rendered entries
-    escaped_orgfile = f"{orgfile}".replace("[1]", "\\[1\\]")
-    assert f":SOURCE: [[file:{escaped_orgfile}::*Heading\\[1\\]" in f"{entries[0]}"
+    assert f":LINE: file://{orgfile}#line=2" in f"{entries[0]}"
+    # LINE link rendered with line number
+    assert f":LINE: file://{orgfile}#line=7" in f"{entries[1]}"
 
 
 # ----------------------------------------------------------------------------------------------------