Use YAML file to allow user to configure application. Add tests

- YAML Config
  - Can specify all params[1] earlier being passed via cmd args in config YAML
  - Can now also configure sentence-transformer models to use etc for search
    - [1] Config params
       - org files
       - compressed entries file config path
       - embeddings file config path

  - Include sample_config.yaml
  - Include sample .org file from this repos readmes

- CLI
  - Configuration Priority: Config via cmd > Config via YAML > Default Config
  - Test CLI, include test config.yml for the tests

- Set default type to None unless set via query param to API
  Run notes search if search_enabled, also if type is None (default)
  Prepares for running queries on all search types unless type
  specified in API query param

- Update Readme

README.org

@@ -18,7 +18,7 @@
    Load ML model, generate embeddings and expose API to query specified org-mode files
 
    #+begin_src shell
-   python3 src/main.py --input-files ~/Notes/Schedule.org ~/Notes/Incoming.org --verbose
+   python3 src/main.py --org-files ~/Notes/Schedule.org ~/Notes/Incoming.org -c sample_config.yml --verbose
    #+end_src
 
 ** Use

environment.yml

@@ -9,4 +9,5 @@ dependencies:
   - sentence-transformers
   - fastapi
   - uvicorn
+  - pyyaml
   - pytest

sample_config.yml

@@ -0,0 +1,11 @@
+content-type:
+  org:
+    input-files: ["src/tests/data/main_readme.org", "src/tests/data/interface_emacs_readme.org"]
+    input-filter: null
+    compressed-jsonl: ".notes.json.gz"
+    embeddings-file: ".note_embeddings.pt"
+
+search-type:
+  asymmetric:
+    encoder: "sentence-transformers/msmarco-MiniLM-L-6-v3"
+    cross-encoder: "cross-encoder/ms-marco-MiniLM-L-6-v2"

src/main.py

@@ -6,12 +6,13 @@ from typing import Optional
 
 # External Packages
 import uvicorn
+import yaml
 from fastapi import FastAPI
 
 # Internal Packages
 from search_type import asymmetric
 from processor.org_mode.org_to_jsonl import org_to_jsonl
-from utils.helpers import is_none_or_empty
+from utils.helpers import is_none_or_empty, get_absolute_path, get_from_dict, merge_dicts
 
 
 app = FastAPI()
@@ -26,7 +27,7 @@ def search(q: str, n: Optional[int] = 5, t: Optional[str] = None):
     user_query = q
     results_count = n
 
-    if t == 'notes' or t == None:
+    if (t == 'notes' or t == None) and notes_search_enabled:
         # query notes
         hits = asymmetric.query_notes(
             user_query,
@@ -45,35 +46,90 @@ def search(q: str, n: Optional[int] = 5, t: Optional[str] = None):
 
 @app.get('/regenerate')
 def regenerate(t: Optional[str] = None):
-    if t == 'notes' or t == None:
+    if (t == 'notes' or t == None) and notes_search_enabled:
         # Extract Entries, Generate Embeddings
         global corpus_embeddings
         global entries
-        entries, corpus_embeddings, _, _, _ = asymmetric.setup(args.input_files, args.input_filter, args.compressed_jsonl, args.embeddings, regenerate=True, verbose=args.verbose)
+        entries, corpus_embeddings, _, _, _ = asymmetric.setup(
+            org_config['input-files'],
+            org_config['input-filter'],
+            pathlib.Path(org_config['compressed-jsonl']),
+            pathlib.Path(org_config['embeddings-file']),
+            regenerate=True,
+            verbose=args.verbose)
+
 
     return {'status': 'ok', 'message': 'regeneration completed'}
 
 
 def cli(args=None):
-    if not args:
+    if is_none_or_empty(args):
         args = sys.argv[1:]
 
     # Setup Argument Parser for the Commandline Interface
     parser = argparse.ArgumentParser(description="Expose API for Semantic Search")
-    parser.add_argument('--input-files', '-i', nargs='*', help="List of org-mode files to process")
-    parser.add_argument('--input-filter', type=str, default=None, help="Regex filter for org-mode files to process")
-    parser.add_argument('--compressed-jsonl', '-j', type=pathlib.Path, default=pathlib.Path(".notes.jsonl.gz"), help="Compressed JSONL formatted notes file to compute embeddings from")
-    parser.add_argument('--embeddings', '-e', type=pathlib.Path, default=pathlib.Path(".notes_embeddings.pt"), help="File to save/load model embeddings to/from")
-    parser.add_argument('--regenerate', action='store_true', default=False, help="Regenerate embeddings from org-mode files. Default: false")
+    parser.add_argument('--org-files', '-i', nargs='*', help="List of org-mode files to process")
+    parser.add_argument('--org-filter', type=str, default=None, help="Regex filter for org-mode files to process")
+    parser.add_argument('--config-file', '-c', type=pathlib.Path, help="YAML file with user configuration")
+    parser.add_argument('--regenerate', action='store_true', default=False, help="Regenerate model embeddings from source files. Default: false")
     parser.add_argument('--verbose', '-v', action='count', default=0, help="Show verbose conversion logs. Default: 0")
+    args = parser.parse_args(args)
 
-    return parser.parse_args(args)
+    if not (args.config_file or args.org_files):
+        print(f"Require at least 1 of --org-file, --org-filter or --config-file flags to be passed from commandline")
+        exit(1)
+
+    # Config Priority: Cmd Args > Config File > Default Config
+    args.config = default_config
+    if args.config_file and args.config_file.exists():
+        with open(get_absolute_path(args.config_file), 'r', encoding='utf-8') as config_file:
+            config_from_file = yaml.safe_load(config_file)
+            args.config = merge_dicts(priority_dict=config_from_file, default_dict=args.config)
+
+    if args.org_files:
+        args.config['content-type']['org']['input-files'] = args.org_files
+
+    if args.org_filter:
+        args.config['content-type']['org']['input-filter'] = args.org_filter
+
+    return args
+
+
+default_config = {
+    'content-type':
+    {
+        'org':
+        {
+            'compressed-jsonl': '.notes.jsonl.gz',
+            'embeddings-file': '.note_embeddings.pt'
+        }
+    },
+    'search-type':
+    {
+        'asymmetric':
+        {
+            'encoder': "sentence-transformers/msmarco-MiniLM-L-6-v3",
+            'cross-encoder': "cross-encoder/ms-marco-MiniLM-L-6-v2"
+        }
+    }
+}
 
 
 if __name__ == '__main__':
     args = cli()
+    org_config = get_from_dict(args.config, 'content-type', 'org')
+
+    notes_search_enabled = False
+    if 'input-files' in org_config or 'input-filter' in org_config:
+        notes_search_enabled = True
+        entries, corpus_embeddings, bi_encoder, cross_encoder, top_k = asymmetric.setup(
+            org_config['input-files'],
+            org_config['input-filter'],
+            pathlib.Path(org_config['compressed-jsonl']),
+            pathlib.Path(org_config['embeddings-file']),
+            args.regenerate,
+            args.verbose)
 
-    entries, corpus_embeddings, bi_encoder, cross_encoder, top_k = asymmetric.setup(args.input_files, args.input_filter, args.compressed_jsonl, args.embeddings, args.regenerate, args.verbose)
 
     # Start Application Server
     uvicorn.run(app)

src/tests/data/config.yml

@@ -0,0 +1,11 @@
+content-type:
+  org:
+    input-files: [ "~/first_from_config.org", "~/second_from_config.org" ]
+    input-filter: "*.org"
+    compressed-jsonl: ".notes.json.gz"
+    embeddings-file: ".note_embeddings.pt"
+
+search-type:
+  asymmetric:
+    encoder: "sentence-transformers/msmarco-MiniLM-L-6-v3"
+    cross-encoder: "cross-encoder/ms-marco-MiniLM-L-6-v2"

src/tests/test_main.py

@@ -32,34 +32,64 @@ def test_asymmetric_setup():
     assert len(corpus_embeddings) == 10
 
 
-# ----------------------------------------------------------------------------------------------------
-def test_cli_default():
+def test_cli_minimal_default():
     # Act
-    args = cli(['--input-files=tests/data/test.org'])
+    actual_args = cli(['--config-file=tests/data/config.yml'])
 
     # Assert
-    assert args.input_files == ['tests/data/test.org']
-    assert args.input_filter == None
-    assert args.compressed_jsonl == Path('.notes.jsonl.gz')
-    assert args.embeddings == Path('.notes_embeddings.pt')
-    assert args.regenerate == False
-    assert args.verbose == 0
-
+    assert actual_args.config_file == Path('tests/data/config.yml')
+    assert actual_args.regenerate == False
+    assert actual_args.verbose == 0
 
 # ----------------------------------------------------------------------------------------------------
-def test_cli_set_by_user():
+def test_cli_flags():
     # Act
-    actual_args = cli(['--input-files=tests/data/test.org',
-                       '--input-filter=tests/data/*.org',
-                       '--compressed-jsonl=tests/data/.test.jsonl.gz',
-                       '--embeddings=tests/data/.test_embeddings.pt',
+    actual_args = cli(['--config-file=tests/data/config.yml',
                        '--regenerate',
                        '-vvv'])
 
     # Assert
-    assert actual_args.input_files == ['tests/data/test.org']
-    assert actual_args.input_filter == 'tests/data/*.org'
-    assert actual_args.compressed_jsonl == Path('tests/data/.test.jsonl.gz')
-    assert actual_args.embeddings == Path('tests/data/.test_embeddings.pt')
+    assert actual_args.config_file == Path('tests/data/config.yml')
     assert actual_args.regenerate == True
     assert actual_args.verbose == 3
+
+
+# ----------------------------------------------------------------------------------------------------
+def test_cli_config_from_file():
+    # Act
+    actual_args = cli(['--config-file=tests/data/config.yml',
+                       '--regenerate',
+                       '-vvv'])
+
+    # Assert
+    assert actual_args.config_file == Path('tests/data/config.yml')
+    assert actual_args.regenerate == True
+    assert actual_args.config is not None
+    assert actual_args.config['content-type']['org']['input-files'] == ['~/first_from_config.org', '~/second_from_config.org']
+    assert actual_args.verbose == 3
+
+
+# ----------------------------------------------------------------------------------------------------
+def test_cli_config_from_cmd_args():
+    ""
+    # Act
+    actual_args = cli(['--org-files=first.org'])
+
+    # Assert
+    assert actual_args.org_files == ['first.org']
+    assert actual_args.config_file is None
+    assert actual_args.config is not None
+    assert actual_args.config['content-type']['org']['input-files'] == ['first.org']
+
+
+# ----------------------------------------------------------------------------------------------------
+def test_cli_config_from_cmd_args_override_config_file():
+    # Act
+    actual_args = cli(['--config-file=tests/data/config.yml',
+                       '--org-files=first.org'])
+
+    # Assert
+    assert actual_args.org_files == ['first.org']
+    assert actual_args.config_file == Path('tests/data/config.yml')
+    assert actual_args.config is not None
+    assert actual_args.config['content-type']['org']['input-files'] == ['first.org']