Merge pull request #63 from TheJacksonLaboratory/G3-324-db-get-genset…

…-arguments

G3-324 get geneset size and date parameters

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "geneweaver-db"
-version = "0.5.0a15"
+version = "0.5.0a16"
 description = "Database Interaction Services for GeneWeaver"
 authors = ["Jax Computational Sciences <[email protected]>"]
 readme = "README.md"

src/geneweaver/db/aio/geneset.py

@@ -1,5 +1,6 @@
 """Async database interaction code relating to Genesets."""
 
+from datetime import date
 from typing import List, Optional
 
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, ScoreType, Species
@@ -25,12 +26,18 @@ async def get(
     pubmed_id: Optional[int] = None,
     gene_id_type: Optional[GeneIdentifier] = None,
     search_text: Optional[str] = None,
-    limit: Optional[int] = None,
-    offset: Optional[int] = None,
     is_readable_by: Optional[int] = None,
     with_publication_info: bool = True,
     ontology_term: Optional[str] = None,
     score_type: Optional[ScoreType] = None,
+    lte_count: Optional[int] = None,
+    gte_count: Optional[int] = None,
+    created_after: Optional[date] = None,
+    created_before: Optional[date] = None,
+    updated_after: Optional[date] = None,
+    updated_before: Optional[date] = None,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
 ) -> List[Row]:
     """Get genesets from the database.
 
@@ -46,12 +53,18 @@ async def get(
     :param gene_id_type: Show only results with this gene ID type.
     :param search_text: Return genesets that match this search text (using PostgreSQL
                         full-text search).
-    :param limit: Limit the number of results.
-    :param offset: Offset the results.
     :param is_readable_by: A user ID to check if the user can read the results.
     :param with_publication_info: Include publication info in the return.
     :param ontology_term: Show only results associated with this ontology term.
     :param score_type: Show only results with given score type.
+    :param lte_count: less than or equal count.
+    :param gte_count: greater than or equal count.
+    :param updated_before: Show only results updated before this date.
+    :param updated_after: Show only results updated after this date.
+    :param created_before: Show only results created before this date.
+    :param created_after: Show only results updated before this date.
+    :param limit: Limit the number of results.
+    :param offset: Offset the results.
 
     :return: list of results using `.fetchall()`
     """
@@ -73,6 +86,12 @@ async def get(
             with_publication_info=with_publication_info,
             ontology_term=ontology_term,
             score_type=score_type,
+            lte_count=lte_count,
+            gte_count=gte_count,
+            created_after=created_after,
+            created_before=created_before,
+            updated_after=updated_after,
+            updated_before=updated_before,
         )
     )
 

src/geneweaver/db/geneset.py

@@ -1,5 +1,6 @@
 """Geneset database functions."""
 
+from datetime import date
 from typing import List, Optional
 
 from geneweaver.core.enum import GeneIdentifier, GenesetTier, ScoreType, Species
@@ -31,6 +32,12 @@ def get(
     with_publication_info: bool = True,
     ontology_term: Optional[str] = None,
     score_type: Optional[ScoreType] = None,
+    lte_count: Optional[int] = None,
+    gte_count: Optional[int] = None,
+    created_after: Optional[date] = None,
+    created_before: Optional[date] = None,
+    updated_after: Optional[date] = None,
+    updated_before: Optional[date] = None,
 ) -> List[Row]:
     """Get genesets from the database.
 
@@ -47,11 +54,17 @@ def get(
     :param gene_id_type: Show only results with this gene ID type.
     :param search_text: Return genesets that match this search text (using PostgreSQL
                         full-text search).
-    :param limit: Limit the number of results.
-    :param offset: Offset the results.
     :param with_publication_info: Include publication info in the return.
     :param ontology_term: Show only results associated with this ontology term.
     :param score_type: Show only results with given score type.
+    :param lte_count: less than or equal count.
+    :param gte_count: greater than or equal count.
+    :param updated_before: Show only results updated before this date.
+    :param updated_after: Show only results updated after this date.
+    :param created_before: Show only results created before this date.
+    :param created_after: Show only results updated before this date.
+    :param limit: Limit the number of results.
+    :param offset: Offset the results.
 
     :return: list of results using `.fetchall()`
     """
@@ -73,6 +86,12 @@ def get(
             with_publication_info=with_publication_info,
             ontology_term=ontology_term,
             score_type=score_type,
+            lte_count=lte_count,
+            gte_count=gte_count,
+            created_after=created_after,
+            created_before=created_before,
+            updated_after=updated_after,
+            updated_before=updated_before,
         )
     )
 

src/geneweaver/db/query/geneset/read.py

@@ -1,5 +1,6 @@
 """SQL query generation code for reading genesets."""
 
+from datetime import date
 from typing import Optional, Tuple
 
 from geneweaver.core.enum import GeneIdentifier, ScoreType, Species
@@ -11,7 +12,7 @@
     restrict_tier,
     search,
 )
-from geneweaver.db.query.utils import construct_filters
+from geneweaver.db.query.utils import construct_filters, construct_op_filters
 from geneweaver.db.utils import GenesetTierOrTiers, limit_and_offset
 from psycopg.sql import SQL, Composed
 
@@ -34,6 +35,12 @@ def get(
     with_publication_info: bool = True,
     ontology_term: Optional[str] = None,
     score_type: Optional[ScoreType] = None,
+    lte_count: Optional[int] = None,
+    gte_count: Optional[int] = None,
+    created_after: Optional[date] = None,
+    created_before: Optional[date] = None,
+    updated_after: Optional[date] = None,
+    updated_before: Optional[date] = None,
 ) -> Tuple[Composed, dict]:
     """Get genesets.
 
@@ -55,6 +62,12 @@ def get(
     :param with_publication_info: Include publication info in the return.
     :param ontology_term: Show only results associated with this ontology term.
     :param score_type: Show only results with given score type.
+    :param lte_count: less than or equal count.
+    :param gte_count: greater than or equal count.
+    :param updated_before: Show only results updated before this date.
+    :param updated_after: Show only results updated after this date.
+    :param created_before: Show only results created before this date.
+    :param created_after: Show only results updated before this date.
     """
     params = {}
     filtering = []
@@ -93,6 +106,49 @@ def get(
         },
     )
 
+    filtering, params = construct_op_filters(
+        filters=filtering,
+        params=params,
+        filter_items=[
+            {
+                "field": "gs_count",
+                "value": lte_count,
+                "op": "<=",
+                "place_holder": "count_less_than",
+            },
+            {
+                "field": "gs_count",
+                "value": gte_count,
+                "op": ">=",
+                "place_holder": "count_greater_than",
+            },
+            {
+                "field": "gs_created",
+                "value": created_before,
+                "op": "<=",
+                "place_holder": "created_before",
+            },
+            {
+                "field": "gs_created",
+                "value": created_after,
+                "op": ">=",
+                "place_holder": "created_after",
+            },
+            {
+                "field": "gs_updated",
+                "value": updated_before,
+                "op": "<=",
+                "place_holder": "updated_before",
+            },
+            {
+                "field": "gs_updated",
+                "value": updated_after,
+                "op": ">=",
+                "place_holder": "updated_after",
+            },
+        ],
+    )
+
     if len(filtering) > 0:
         query += SQL("WHERE") + SQL("AND").join(filtering)
 

src/geneweaver/db/query/utils.py

@@ -8,30 +8,45 @@
 SQLList = List[Union[Composed, SQL]]
 ParamDict = Dict[str, Union[str, int, list]]
 OptionalParamDict = Dict[str, Optional[Union[str, int]]]
+OptionalParamTuple = Tuple[str, Optional[Union[str, int]]]
 
 
 def construct_filter(
     filters: SQLList,
     params: ParamDict,
     filter_name: str,
     filter_value: Optional[Union[str, int]],
+    operator: Optional[str] = None,
+    place_holder: Optional[str] = None,
 ) -> Tuple[SQLList, ParamDict]:
     """Construct a simple filter for a query.
 
     :param filters: The existing filters.
     :param params: The existing parameters.
     :param filter_name: The filter name to construct.
     :param filter_value: The filter value to construct.
+    :param operator: sql operator
+    :param place_holder: parameter placeholder name
 
     :return: The constructed filters and parameters.
+
     """
+    if place_holder is None:
+        place_holder = filter_name
+
     if filter_value is not None:
+        if operator:
+            filter_str = "{filter_name} " + operator + " {param_name}"
+        else:
+            filter_str = "{filter_name} = {param_name}"
+
         filters.append(
-            SQL("{filter_name} = {param_name}").format(
-                filter_name=Identifier(filter_name), param_name=Placeholder(filter_name)
+            SQL(filter_str).format(
+                filter_name=Identifier(filter_name),
+                param_name=Placeholder(place_holder),
             )
         )
-        params[filter_name] = filter_value
+        params[place_holder] = filter_value
     return filters, params
 
 
@@ -61,6 +76,36 @@ def construct_filters(
     return filters, params
 
 
+def construct_op_filters(
+    filters: SQLList,
+    params: ParamDict,
+    filter_items: [dict],
+) -> Tuple[SQLList, ParamDict]:
+    """Construct multiple simple filters with operators for a query.
+
+    Calls the `construct_filter` function for each filter item.
+
+    :param filters: The existing filters.
+    :param params: The existing parameters.
+    :param filter_items: The filter items to construct.
+
+    :return: The constructed filters and parameters.
+    """
+    for filter_item in filter_items:
+        filters, params = construct_filter(
+            filters=filters,
+            params=params,
+            filter_name=filter_item.get("field"),
+            filter_value=filter_item.get("value"),
+            operator=filter_item.get("op"),
+            place_holder=filter_item.get("place_holder"),
+        )
+
+    print(filters)
+    print(params)
+    return filters, params
+
+
 def search(
     field_ts_vector: str,
     existing_filters: SQLList,

tests/unit/geneset/test_get.py

@@ -1,5 +1,8 @@
 """Test the general geneset.get function."""
 
+import datetime
+
+import pytest
 from geneweaver.db.aio.geneset import get as async_get
 from geneweaver.db.geneset import get
 
@@ -25,3 +28,39 @@
 test_async_get_fetchall_raises_error = async_create_fetchall_raises_error_test(
     async_get,
 )
+
+
+@pytest.mark.parametrize("created_after", [None, datetime.datetime(2008, 7, 31)])
+@pytest.mark.parametrize("created_before", [None, datetime.datetime(2024, 7, 31)])
+def test_get_gs_by_create_date(created_before, created_after, example_genesets, cursor):
+    """Test the geneset.get function by create date using a mock cursor."""
+    cursor.fetchall.return_value = example_genesets
+    result = get(cursor, created_before=created_before, created_after=created_after)
+    assert result == example_genesets
+    assert cursor.execute.call_count == 1
+    assert cursor.fetchone.call_count == 0
+    assert cursor.fetchall.call_count == 1
+
+
+@pytest.mark.parametrize("updated_after", [None, datetime.datetime(2008, 7, 31)])
+@pytest.mark.parametrize("updated_before", [None, datetime.datetime(2024, 7, 31)])
+def test_get_gs_by_update_date(updated_before, updated_after, example_genesets, cursor):
+    """Test the geneset.get function by update date a mock cursor."""
+    cursor.fetchall.return_value = example_genesets
+    result = get(cursor, updated_before=updated_before, updated_after=updated_after)
+    assert result == example_genesets
+    assert cursor.execute.call_count == 1
+    assert cursor.fetchone.call_count == 0
+    assert cursor.fetchall.call_count == 1
+
+
+@pytest.mark.parametrize("lte_count", [None, 20])
+@pytest.mark.parametrize("gte_count", [None, 5])
+def test_get_gs_gense_count_size(lte_count, gte_count, example_genesets, cursor):
+    """Test the geneset.get function by update date a mock cursor."""
+    cursor.fetchall.return_value = example_genesets
+    result = get(cursor, lte_count=lte_count, gte_count=gte_count)
+    assert result == example_genesets
+    assert cursor.execute.call_count == 1
+    assert cursor.fetchone.call_count == 0
+    assert cursor.fetchall.call_count == 1