Merge pull request #2 from linkml/mongodb

first pass at mongodb (authored by Claude)

Makefile

@@ -15,7 +15,7 @@ all-pytest:
 	$(RUN) pytest -m "integration or not integration"
 
 install-all:
-	poetry install -E analytics -E app -E tests -E llm
+	poetry install -E analytics -E app -E tests -E llm -E mongodb
 
 # not yet deployed
 doctest:

docs/examples/Tutorial.ipynb

@@ -42,7 +42,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "## Attach and populate a DuckDB in-memory databse\n",
+    "## Attach and populate a DuckDB in-memory database\n",
     "\n",
     "Here we will create/attach a database to the client, and populate it\n",
     "with some JSON objects. Note that for this example, we don't provide a schema - this is *induced* behind the scenes\n",

pyproject.toml

@@ -21,6 +21,7 @@ plotly = { version = "*", optional = true }
 pystow = "^0.5.4"
 black = { version=">=24.0.0", optional = true }
 llm = { version="*", optional = true }
+pymongo = { version="*", optional = true }
 pandas = "^2.2.1"
 
 [tool.poetry.group.dev.dependencies]
@@ -48,6 +49,7 @@ analytics = ["pandas", "matplotlib", "seaborn", "plotly"]
 app = ["streamlit"]
 tests = ["black"]
 llm = ["llm"]
+mongodb = ["pymongo"]
 
 [tool.poetry.scripts]
 linkml-store = "linkml_store.cli:main"
@@ -109,7 +111,7 @@ max-complexity = 10
 
 [tool.codespell]
 # TODO: bring in tests in too
-skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock'
+skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock,*.ipynb'
 # Ignore table where words could be split across rows
 # Ignore shortcut specifications like [Ff]alse
 ignore-regex = '(\|.*\|.*\|.*\||\[[A-Z][a-z]\][a-z][a-z])'

src/linkml_data_browser/__init__.py

@@ -1,2 +1 @@
 """linkml-data-browser package."""
-

src/linkml_data_browser/app.py

@@ -33,9 +33,7 @@ def init_reset_filters(cd: ClassDefinition, reset=False):
             st.session_state[key] = ""  # Assuming text input, adjust for other types
 
 
-def apply_filters(
-    collection: Collection, filters: Dict[str, Any], offset: int, limit: int, **kwargs
-):
+def apply_filters(collection: Collection, filters: Dict[str, Any], offset: int, limit: int, **kwargs):
     print(f"FILTERS={filters}")
     return collection.find(filters, offset=offset, limit=limit, **kwargs)
 
@@ -44,7 +42,7 @@ def render_filter_widget(collection: Collection, attribute: SlotDefinition):
     """Render appropriate Streamlit widget based on column type."""
     logger.info("Rendering filter widget")
     # print(f"{attribute.name} // RANGE={attribute.range}")
-    col_type = attribute.range
+    # col_type = attribute.range
     col_name = attribute.name
     cols = st.sidebar.columns([1, 10])
     with cols[0]:
@@ -58,7 +56,7 @@ def render_filter_widget(collection: Collection, attribute: SlotDefinition):
     with cols[1]:
         filter_value = st.text_input(f"Filter by {col_name}", key=f"filter_{col_name}")
     return filter_value
-    #return st.sidebar.text_input(f"Filter by {col_name}")
+    # return st.sidebar.text_input(f"Filter by {col_name}")
     # elif col_type == "integer":
     #     max_value = con.execute(f"SELECT MAX({col_name}) FROM {tbl_name}").fetchall()[0][0]
     #     min_value = con.execute(f"SELECT MIN({col_name}) FROM {tbl_name}").fetchall()[0][0]
@@ -109,7 +107,7 @@ def main():
         if prev_value != new_value:
             # print(f"CHANGE FOR {att_name}: {prev_value} -> {new_value}")
             filter_changed = True
-            #st.session_state[key] = new_value
+            # st.session_state[key] = new_value
         facet_key = f"facet_view_{att_name}"
         if facet_key in st.session_state and st.session_state[facet_key]:
             facet_results = collection.query_facets(filters, facet_columns=[att_name])

src/linkml_store/__init__.py

@@ -1,7 +1,7 @@
 from pathlib import Path
+
 from linkml_store.api import Client
 
 THIS_DIR = Path(__file__).parent
 
 __all__ = ["Client"]
-

src/linkml_store/api/__init__.py

@@ -1,6 +1,8 @@
+# flake8: noqa: E402
 from linkml_store.api.collection import Collection
 from linkml_store.api.database import Database
 from linkml_store.api.metadata import MetaData
 from linkml_store.api.client import Client
+# flake8: noqa
 
 __all__ = ["Client", "Database", "MetaData", "Collection"]

src/linkml_store/api/client.py

@@ -42,7 +42,12 @@ class Client:
     _databases: Optional[Dict[str, Database]] = None
 
     def attach_database(
-        self, handle: str, alias: Optional[str] = None, schema_view: Optional[SchemaView] = None, recreate_if_exists=False, **kwargs
+        self,
+        handle: str,
+        alias: Optional[str] = None,
+        schema_view: Optional[SchemaView] = None,
+        recreate_if_exists=False,
+        **kwargs,
     ) -> Database:
         """
         Associate a database with a handle.