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Index Parent Headings of Org-Mode Entries to Improve Search Context (#548)

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### Overview
The parent hierarchy of org-mode entries can store important context. 
This change updates OrgNode to track parent headings for each org entry and adds the parent outline for each entry to the index

### Details
- Test search uses ancestor headings as context for improved results
- Add ancestor headings of each org-mode entry to their compiled form
- Track ancestor headings for each org-mode entry in org-node parser

Resolves #85
This commit is contained in:
Debanjum 2023-11-19 13:18:19 -08:00 committed by GitHub
commit 71799add0b
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10 changed files with 215 additions and 40 deletions
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11
src/khoj/processor/org_mode/org_to_entries.py
View file

@ -100,16 +100,17 @@ class OrgToEntries(TextToEntries):
continue
todo_str = f"{parsed_entry.todo} " if parsed_entry.todo else ""
# Prepend filename as top heading to entry
filename = Path(entry_to_file_map[parsed_entry]).stem
# Prepend ancestor headings, filename as top heading to entry for context
ancestors_trail = " / ".join(parsed_entry.ancestors) or Path(entry_to_file_map[parsed_entry])
if parsed_entry.heading:
heading = f"* {filename}\n** {todo_str}{parsed_entry.heading}."
heading = f"* Path: {ancestors_trail}\n** {todo_str}{parsed_entry.heading}."
else:
heading = f"* {filename}."
heading = f"* Path: {ancestors_trail}."
compiled = heading
if state.verbose > 2:
logger.debug(f"Title: {parsed_entry.heading}")
logger.debug(f"Title: {heading}")
if parsed_entry.tags:
tags_str = " ".join(parsed_entry.tags)

38
src/khoj/processor/org_mode/orgnode.py
View file

@ -80,6 +80,7 @@ def makelist(file, filename):
} # populated from #+SEQ_TODO line
level = ""
heading = ""
ancestor_headings = []
bodytext = ""
introtext = ""
tags = list() # set of all tags in headline
@ -98,7 +99,7 @@ def makelist(file, filename):
heading_search = re.search(r"^(\*+)\s(.*?)\s*$", line)
if heading_search: # we are processing a heading line
if heading: # if we have are on second heading, append first heading to headings list
thisNode = Orgnode(level, heading, bodytext, tags)
thisNode = Orgnode(level, heading, bodytext, tags, ancestor_headings)
if closed_date:
thisNode.closed = closed_date
closed_date = ""
@ -114,6 +115,8 @@ def makelist(file, filename):
thisNode.properties = property_map
nodelist.append(thisNode)
property_map = {"LINE": f"file:{normalize_filename(filename)}::{ctr}"}
previous_level = level
previous_heading = heading
level = heading_search.group(1)
heading = heading_search.group(2)
bodytext = ""
@ -126,6 +129,17 @@ def makelist(file, filename):
for parsedtag in parsedtags.split(":"):
if parsedtag != "":
tags.append(parsedtag)
# Add previous heading to ancestors if current heading is deeper than previous level
if len(level) > len(previous_level) and previous_heading:
ancestor_headings.append(previous_heading)
# Remove last ancestor(s) if current heading is shallower than previous level
elif len(level) < len(previous_level):
for _ in range(len(level), len(previous_level)):
if not ancestor_headings or len(ancestor_headings) == 0:
break
ancestor_headings.pop()
else: # we are processing a non-heading line
if line[:10] == "#+SEQ_TODO":
kwlist = re.findall(r"([A-Z]+)\(", line)
@ -216,7 +230,7 @@ def makelist(file, filename):
nodelist = [thisNode] + nodelist
# write out last heading node
if heading:
thisNode = Orgnode(level, heading, bodytext, tags)
thisNode = Orgnode(level, heading, bodytext, tags, ancestor_headings)
thisNode.properties = property_map
if sched_date:
thisNode.scheduled = sched_date
@ -243,6 +257,9 @@ def makelist(file, filename):
n.priority = priority_search.group(1)
n.heading = priority_search.group(2)
# 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"
@ -261,7 +278,7 @@ class Orgnode(object):
with the headline.
"""
def __init__(self, level, headline, body, tags):
def __init__(self, level, headline, body, tags, ancestor_headings=[]):
"""
Create an Orgnode object given the parameters of level (as the
raw asterisks), headline text (including the TODO tag), and
@ -279,8 +296,21 @@ class Orgnode(object):
self._closed = "" # Closed date
self._properties = dict()
self._logbook = list() # List of clock-in, clock-out tuples representing logbook entries
self._ancestor_headings = ancestor_headings.copy()
# Look for priority in headline and transfer to prty field
@property
def ancestors(self) -> List[str]:
"""
Return the ancestor headings of the node
"""
return self._ancestor_headings
@ancestors.setter
def ancestors(self, new_ancestors):
"""
Update the ancestor headings of the node
"""
self._ancestor_headings = new_ancestors
@property
def heading(self):

41
tests/conftest.py
View file

@ -384,6 +384,45 @@ def sample_org_data():
def get_sample_data(type):
sample_data = {
"org": {
"elisp.org": """
* Emacs Khoj
/An Emacs interface for [[https://github.com/khoj-ai/khoj][khoj]]/
** Requirements
- Install and Run [[https://github.com/khoj-ai/khoj][khoj]]
** Installation
*** Direct
- Put ~khoj.el~ in your Emacs load path. For e.g ~/.emacs.d/lisp
- Load via ~use-package~ in your ~/.emacs.d/init.el or .emacs file by adding below snippet
#+begin_src elisp
;; Khoj Package
(use-package khoj
:load-path "~/.emacs.d/lisp/khoj.el"
:bind ("C-c s" . 'khoj))
#+end_src
*** Using [[https://github.com/quelpa/quelpa#installation][Quelpa]]
- Ensure [[https://github.com/quelpa/quelpa#installation][Quelpa]], [[https://github.com/quelpa/quelpa-use-package#installation][quelpa-use-package]] are installed
- Add below snippet to your ~/.emacs.d/init.el or .emacs config file and execute it.
#+begin_src elisp
;; Khoj Package
(use-package khoj
:quelpa (khoj :fetcher url :url "https://raw.githubusercontent.com/khoj-ai/khoj/master/interface/emacs/khoj.el")
:bind ("C-c s" . 'khoj))
#+end_src
** Usage
1. Call ~khoj~ using keybinding ~C-c s~ or ~M-x khoj~
2. Enter Query in Natural Language
e.g "What is the meaning of life?" "What are my life goals?"
3. Wait for results
*Note: It takes about 15s on a Mac M1 and a ~100K lines corpus of org-mode files*
4. (Optional) Narrow down results further
Include/Exclude specific words from results by adding to query
e.g "What is the meaning of life? -god +none"
""",
"readme.org": """
* Khoj
/Allow natural language search on user content like notes, images using transformer based models/
@ -399,7 +438,7 @@ def get_sample_data(type):
git clone https://github.com/khoj-ai/khoj && cd khoj
conda env create -f environment.yml
conda activate khoj
#+end_src"""
#+end_src""",
},
"markdown": {
"readme.markdown": """

14
tests/data/org/interface_emacs_readme.org vendored
View file

@ -4,10 +4,9 @@
** Requirements
- Install and Run [[https://github.com/khoj-ai/khoj][khoj]]
** Installation
- Direct Install
** Install
*** Direct
- Put ~khoj.el~ in your Emacs load path. For e.g ~/.emacs.d/lisp
- Load via ~use-package~ in your ~/.emacs.d/init.el or .emacs file by adding below snippet
#+begin_src elisp
;; Khoj Package
@ -16,7 +15,7 @@
:bind ("C-c s" . 'khoj))
#+end_src
- Use [[https://github.com/quelpa/quelpa#installation][Quelpa]]
*** Using [[https://github.com/quelpa/quelpa#installation][Quelpa]]
- Ensure [[https://github.com/quelpa/quelpa#installation][Quelpa]], [[https://github.com/quelpa/quelpa-use-package#installation][quelpa-use-package]] are installed
- Add below snippet to your ~/.emacs.d/init.el or .emacs config file and execute it.
#+begin_src elisp
@ -28,17 +27,10 @@
** Usage
1. Call ~khoj~ using keybinding ~C-c s~ or ~M-x khoj~
2. Enter Query in Natural Language
e.g "What is the meaning of life?" "What are my life goals?"
3. Wait for results
*Note: It takes about 15s on a Mac M1 and a ~100K lines corpus of org-mode files*
4. (Optional) Narrow down results further
Include/Exclude specific words from results by adding to query
e.g "What is the meaning of life? -god +none"

6
tests/data/org/main_readme.org vendored
View file

@ -22,16 +22,16 @@
#+end_src
** Use
- *Khoj via Emacs*
*** *Khoj via Emacs*
- [[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~
- *Khoj via API*
*** *Khoj via API*
- Query: ~GET~ [[http://localhost:42110/api/search?q=%22what%20is%20the%20meaning%20of%20life%22][http://localhost:42110/api/search?q="What is the meaning of life"]]
- Update Index: ~GET~ [[http://localhost:42110/api/update][http://localhost:42110/api/update]]
- [[http://localhost:42110/docs][Khoj API Docs]]
- *Call Khoj via Python Script Directly*
*** *Call Khoj via Python Script Directly*
#+begin_src shell
python3 search_types/asymmetric.py \
--compressed-jsonl .notes.jsonl.gz \

23
tests/test_client.py
View file

@ -321,7 +321,7 @@ def test_notes_search_with_include_filter(client, sample_org_data, default_user:
assert response.status_code == 200
# assert actual_data contains word "Emacs"
search_result = response.json()[0]["entry"]
assert "Emacs" in search_result
assert "emacs" in search_result
# ----------------------------------------------------------------------------------------------------
@ -347,6 +347,27 @@ def test_notes_search_with_exclude_filter(client, sample_org_data, default_user:
assert "clone" not in search_result
# ----------------------------------------------------------------------------------------------------
@pytest.mark.django_db(transaction=True)
def test_notes_search_requires_parent_context(
client, search_config: SearchConfig, sample_org_data, default_user: KhojUser
):
# Arrange
headers = {"Authorization": "Bearer kk-secret"}
text_search.setup(OrgToEntries, sample_org_data, regenerate=False, user=default_user)
user_query = quote("Install Khoj on Emacs")
# Act
response = client.get(f"/api/search?q={user_query}&n=1&t=org&r=true&max_distance=0.18", headers=headers)
# Assert
assert response.status_code == 200
assert len(response.json()) == 1, "Expected only 1 result"
search_result = response.json()[0]["entry"]
assert "Emacs load path" in search_result, "Expected 'Emacs load path' in search result"
# ----------------------------------------------------------------------------------------------------
@pytest.mark.django_db(transaction=True)
def test_different_user_data_not_accessed(client, sample_org_data, default_user: KhojUser):

2
tests/test_multiple_users.py
View file

@ -69,7 +69,7 @@ def test_index_update_with_user2_inaccessible_user1(client, api_user2: KhojApiUs
# Assert
assert update_response.status_code == 200
assert len(results) == 4
assert len(results) == 5
for result in results:
assert result["additional"]["file"] not in source_file_symbol

5
tests/test_org_to_entries.py
View file

@ -45,9 +45,10 @@ def test_configure_heading_entry_to_jsonl(tmp_path):
assert is_none_or_empty(jsonl_data)
def test_entry_split_when_exceeds_max_words(tmp_path):
def test_entry_split_when_exceeds_max_words():
"Ensure entries with compiled words exceeding max_words are split."
# Arrange
tmp_path = "/tmp/test.org"
entry = f"""*** Heading
\t\r
Body Line
@ -55,7 +56,7 @@ def test_entry_split_when_exceeds_max_words(tmp_path):
data = {
f"{tmp_path}": entry,
}
expected_heading = f"* {tmp_path.stem}\n** Heading"
expected_heading = f"* Path: {tmp_path}\n** Heading"
# Act
# Extract Entries from specified Org files

91
tests/test_orgnode.py
View file

@ -161,6 +161,8 @@ Body Line 1"""
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]}"
@ -260,6 +262,7 @@ Body Line 1"""
assert entries[0].closed == ""
assert entries[0].scheduled == ""
assert entries[0].deadline == ""
assert entries[0].ancestors == ["test"]
# ----------------------------------------------------------------------------------------------------
@ -284,6 +287,7 @@ Body Line 1
assert entries[0].closed == ""
assert entries[0].scheduled == ""
assert entries[0].deadline == ""
assert entries[0].ancestors == ["title1 title2"]
# ----------------------------------------------------------------------------------------------------
@ -304,8 +308,10 @@ entry body
assert len(entries) == 2
assert entries[0].heading == "Title"
assert entries[0].body == "intro body\n"
assert entries[0].ancestors == ["Title"]
assert entries[1].heading == "Entry Heading"
assert entries[1].body == "entry body\n\n"
assert entries[1].ancestors == ["Title"]
# ----------------------------------------------------------------------------------------------------
@ -326,8 +332,93 @@ entry body
assert len(entries) == 2
assert entries[0].heading == "Title1 Title2"
assert entries[0].body == "intro body\n"
assert entries[0].ancestors == ["Title1 Title2"]
assert entries[1].heading == "Entry Heading"
assert entries[1].body == "entry body\n\n"
assert entries[0].ancestors == ["Title1 Title2"]
# ----------------------------------------------------------------------------------------------------
def test_parse_org_with_single_ancestor_heading(tmp_path):
"Parse org entries with parent headings context"
# Arrange
body = f"""
* Heading 1
body 1
** Sub Heading 1
"""
orgfile = create_file(tmp_path, body)
# Act
entries = orgnode.makelist_with_filepath(orgfile)
# Assert
assert len(entries) == 2
assert entries[0].heading == "Heading 1"
assert entries[0].ancestors == [f"{orgfile}"]
assert entries[1].heading == "Sub Heading 1"
assert entries[1].ancestors == [f"{orgfile}", "Heading 1"]
# ----------------------------------------------------------------------------------------------------
def test_parse_org_with_multiple_ancestor_headings(tmp_path):
"Parse org entries with parent headings context"
# Arrange
body = f"""
* Heading 1
body 1
** Sub Heading 1
*** Sub Sub Heading 1
sub sub body 1
"""
orgfile = create_file(tmp_path, body)
# Act
entries = orgnode.makelist_with_filepath(orgfile)
# Assert
assert len(entries) == 3
assert entries[0].heading == "Heading 1"
assert entries[0].ancestors == [f"{orgfile}"]
assert entries[1].heading == "Sub Heading 1"
assert entries[1].ancestors == [f"{orgfile}", "Heading 1"]
assert entries[2].heading == "Sub Sub Heading 1"
assert entries[2].ancestors == [f"{orgfile}", "Heading 1", "Sub Heading 1"]
# ----------------------------------------------------------------------------------------------------
def test_parse_org_with_multiple_ancestor_headings_of_siblings(tmp_path):
"Parse org entries with parent headings context"
# Arrange
body = f"""
* Heading 1
body 1
** Sub Heading 1
*** Sub Sub Heading 1
sub sub body 1
*** Sub Sub Heading 2
** Sub Heading 2
*** Sub Sub Heading 3
"""
orgfile = create_file(tmp_path, body)
# Act
entries = orgnode.makelist_with_filepath(orgfile)
# Assert
assert len(entries) == 6
assert entries[0].heading == "Heading 1"
assert entries[0].ancestors == [f"{orgfile}"]
assert entries[1].heading == "Sub Heading 1"
assert entries[1].ancestors == [f"{orgfile}", "Heading 1"]
assert entries[2].heading == "Sub Sub Heading 1"
assert entries[2].ancestors == [f"{orgfile}", "Heading 1", "Sub Heading 1"]
assert entries[3].heading == "Sub Sub Heading 2"
assert entries[3].ancestors == [f"{orgfile}", "Heading 1", "Sub Heading 1"]
assert entries[4].heading == "Sub Heading 2"
assert entries[4].ancestors == [f"{orgfile}", "Heading 1"]
assert entries[5].heading == "Sub Sub Heading 3"
assert entries[5].ancestors == [f"{orgfile}", "Heading 1", "Sub Heading 2"]
# Helper Functions

24
tests/test_text_search.py
View file

@ -70,7 +70,7 @@ def test_text_search_setup_with_empty_file_creates_no_entries(
text_search.setup(OrgToEntries, data, regenerate=True, user=default_user)
# Assert
assert "Deleted 3 entries. Created 0 new entries for user " in caplog.records[-1].message
assert "Deleted 8 entries. Created 0 new entries for user " in caplog.records[-1].message
verify_embeddings(0, default_user)
@ -90,7 +90,7 @@ def test_text_indexer_deletes_embedding_before_regenerate(
# Assert
assert "Deleting all entries for file type org" in caplog.text
assert "Deleted 3 entries. Created 10 new entries for user " in caplog.records[-1].message
assert "Deleted 8 entries. Created 13 new entries for user " in caplog.records[-1].message
# ----------------------------------------------------------------------------------------------------
@ -106,7 +106,7 @@ def test_text_search_setup_batch_processes(content_config: ContentConfig, defaul
text_search.setup(OrgToEntries, data, regenerate=True, user=default_user)
# Assert
assert "Deleted 3 entries. Created 10 new entries for user " in caplog.records[-1].message
assert "Deleted 8 entries. Created 13 new entries for user " in caplog.records[-1].message
# ----------------------------------------------------------------------------------------------------
@ -161,7 +161,7 @@ async def test_text_search(search_config: SearchConfig):
default_user,
)
query = "How to git install application?"
query = "Load Khoj on Emacs?"
# Act
hits = await text_search.query(default_user, query)
@ -170,7 +170,7 @@ async def test_text_search(search_config: SearchConfig):
# Assert
search_result = results[0].entry
assert "git clone" in search_result, 'search result did not contain "git clone" entry'
assert "Emacs load path" in search_result, 'Expected "Emacs load path" in entry'
# ----------------------------------------------------------------------------------------------------
@ -284,9 +284,9 @@ def test_regenerate_index_with_new_entry(
final_logs = caplog.text
# Assert
assert "Deleted 3 entries. Created 10 new entries for user " in initial_logs
assert "Deleted 10 entries. Created 11 new entries for user " in final_logs
verify_embeddings(11, default_user)
assert "Deleted 8 entries. Created 13 new entries for user " in initial_logs
assert "Deleted 13 entries. Created 14 new entries for user " in final_logs
verify_embeddings(14, default_user)
# ----------------------------------------------------------------------------------------------------
@ -320,7 +320,7 @@ def test_update_index_with_duplicate_entries_in_stable_order(
# Assert
# verify only 1 entry added even if there are multiple duplicate entries
assert "Deleted 3 entries. Created 1 new entries for user " in initial_logs
assert "Deleted 8 entries. Created 1 new entries for user " in initial_logs
assert "Deleted 0 entries. Created 0 new entries for user " in final_logs
verify_embeddings(1, default_user)
@ -357,7 +357,7 @@ def test_update_index_with_deleted_entry(org_config_with_only_new_file: LocalOrg
# Assert
# verify only 1 entry added even if there are multiple duplicate entries
assert "Deleted 3 entries. Created 2 new entries for user " in initial_logs
assert "Deleted 8 entries. Created 2 new entries for user " in initial_logs
assert "Deleted 1 entries. Created 0 new entries for user " in final_logs
verify_embeddings(1, default_user)
@ -388,9 +388,9 @@ def test_update_index_with_new_entry(content_config: ContentConfig, new_org_file
final_logs = caplog.text
# Assert
assert "Deleted 3 entries. Created 10 new entries for user " in initial_logs
assert "Deleted 8 entries. Created 13 new entries for user " in initial_logs
assert "Deleted 0 entries. Created 1 new entries for user " in final_logs
verify_embeddings(11, default_user)
verify_embeddings(14, default_user)
# ----------------------------------------------------------------------------------------------------