Merge pull request #30 from TheJacksonLaboratory/task/prepare-for-0-3…

…-0-release

Task/prepare for 0 3 0 release

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

@@ -83,6 +83,19 @@ def get(
     return query, params
 
 
+def shared_with_user(
+    user_id: int,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+    with_publication_info: bool = True,
+) -> Tuple[Composed, dict]:
+    """Get Genesets that are shared with a user.
+
+    NOTE: NOT IMPLEMENTED
+    """
+    raise NotImplementedError()
+
+
 def by_project_id(
     project_id: int,
     limit: Optional[int] = None,

src/geneweaver/db/query/project.py

@@ -0,0 +1,46 @@
+"""Query generation functions for projects."""
+
+from typing import Optional, Tuple
+
+from psycopg.sql import Composed
+
+
+def get(
+    project_id: Optional[int] = None,
+    owner_id: Optional[int] = None,
+    name: Optional[str] = None,
+    starred: Optional[bool] = None,
+    search_text: Optional[str] = None,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> Tuple[Composed, dict]:
+    """Get projects by any filtering criteria.
+
+    NOTE: NOT IMPLEMENTED
+    """
+    raise NotImplementedError()
+
+
+def shared_with_user(
+    user_id: int,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> Tuple[Composed, dict]:
+    """Get project that are shared with a user.
+
+    NOTE: NOT IMPLEMENTED
+    """
+    raise NotImplementedError()
+
+
+def add(
+    user_id: int,
+    name: str,
+    notes: str,
+    starred: bool = False,
+) -> Tuple[Composed, dict]:
+    """Add a new publication.
+
+    NOTE: NOT IMPLEMENTED
+    """
+    raise NotImplementedError()

src/geneweaver/db/query/publication.py

@@ -31,6 +31,28 @@
 )
 
 
+def get(
+    pub_id: Optional[int] = None,
+    authors: Optional[str] = None,
+    title: Optional[str] = None,
+    abstract: Optional[str] = None,
+    journal: Optional[str] = None,
+    volume: Optional[str] = None,
+    pages: Optional[str] = None,
+    month: Optional[str] = None,
+    year: Optional[str] = None,
+    pubmed: Optional[str] = None,
+    search_text: Optional[str] = None,
+    limit: Optional[int] = None,
+    offset: Optional[int] = None,
+) -> Tuple[Composed, dict]:
+    """Get publications by some criteria.
+
+    NOTE: NOT IMPLEMENTED
+    """
+    raise NotImplementedError()
+
+
 def by_id(pub_id: int) -> Optional[rows.Row]:
     """Create a psycopg query to get a publication by ID.
 

tests/unit/query/geneset/test_shared_with_user.py

@@ -0,0 +1,10 @@
+"""Test the geneset.shared_with_user query function."""
+
+import pytest
+from geneweaver.db.query.geneset.read import shared_with_user
+
+
+def test_shared_with_user_raises_not_implemented():
+    """Test that the shared_with_user function raises a NotImplementedError."""
+    with pytest.raises(NotImplementedError):
+        _ = shared_with_user(user_id=1)

tests/unit/query/project/__init__.py

@@ -0,0 +1 @@
+"""Tests for the project query module."""

tests/unit/query/project/test_add.py

@@ -0,0 +1,10 @@
+"""Test the project.add query generation function."""
+
+import pytest
+from geneweaver.db.query.project import add
+
+
+def test_add_raise_not_implemented():
+    """Test that the add function raises a NotImplementedError."""
+    with pytest.raises(NotImplementedError):
+        _ = add(user_id=1, name="test", notes="notes", starred=True)

tests/unit/query/project/test_get.py

@@ -0,0 +1,18 @@
+"""Test the project.get query generation function."""
+
+import pytest
+from geneweaver.db.query.project import get
+
+
+def test_get_raise_not_implemented():
+    """Test that the get function raises a NotImplementedError."""
+    with pytest.raises(NotImplementedError):
+        _ = get(
+            project_id=1,
+            owner_id=1,
+            name="test",
+            starred=True,
+            search_text="search",
+            limit=1,
+            offset=10,
+        )

tests/unit/query/project/test_shared_with_user.py

@@ -0,0 +1,14 @@
+"""Test the project.shared_with_user query generation function."""
+
+import pytest
+from geneweaver.db.query.project import shared_with_user
+
+
+def test_shared_with_user_raise_not_implemented():
+    """Test that the shared_with_user function raises a NotImplementedError."""
+    with pytest.raises(NotImplementedError):
+        _ = shared_with_user(
+            user_id=1,
+            limit=1,
+            offset=10,
+        )

tests/unit/query/publication/__init__.py

@@ -0,0 +1 @@
+"""Tests for the publication query generation functions."""

tests/unit/query/publication/test_add.py

@@ -0,0 +1,51 @@
+"""Test the publication.add query generation function."""
+
+import pytest
+from geneweaver.db.query.publication import add
+from psycopg.sql import SQL, Composed, Identifier, Placeholder
+
+
+@pytest.mark.parametrize(
+    "authors",
+    ["Author 1", "Author 1, Author 2", "Author 1, Author 2, Author 3, et al."],
+)
+@pytest.mark.parametrize(
+    "title", ["Title 1", "Title 1: Subtitle", "Title 1: Subtitle, Part 2"]
+)
+@pytest.mark.parametrize(
+    "abstract",
+    [
+        "Abstract 1",
+        "Abstract 1: Subabstract",
+        "Abstract 1: Subabstract, Part 2",
+        "A very long abstract" * 100,
+    ],
+)
+@pytest.mark.parametrize(
+    "journal", ["Journal 1", "Journal 1: Subjournal", "Journal 1: Subjournal, Part 2"]
+)
+@pytest.mark.parametrize(
+    "pubmed_id", ["12345678", "23456789", "34567890", "45678901", "1234"]
+)
+def test_add_types(authors, title, abstract, journal, pubmed_id):
+    """Test the add query generation function."""
+    query, params = add(authors, title, abstract, journal, pubmed_id)
+    assert isinstance(query, Composed)
+    assert isinstance(params, dict)
+    for item in query:
+        assert any(
+            isinstance(item, t) for t in [SQL, Composed, Identifier, Placeholder]
+        )
+
+    for item in params.values():
+        if item is not None:
+            assert isinstance(item, str)
+            assert item in [authors, title, abstract, journal, pubmed_id]
+
+    values = [item for item in params.values() if item is not None]
+    assert len(values) == 5
+    assert authors in values
+    assert title in values
+    assert abstract in values
+    assert journal in values
+    assert pubmed_id in values

tests/unit/query/publication/test_get.py

@@ -0,0 +1,10 @@
+"""Test the publication.get query function."""
+
+import pytest
+from geneweaver.db.query.publication import get
+
+
+def test_get_raises_not_implemented():
+    """Test that the get function raises a NotImplementedError."""
+    with pytest.raises(NotImplementedError):
+        _ = get()

tests/unit/query/publication/test_pub_insert_cols.py

@@ -0,0 +1,24 @@
+"""Test the PUB_INSERT_COLS generated constant."""
+
+from psycopg.sql import SQL, Identifier
+
+
+def test_pub_insert_cols_types():
+    """Test the PUB_INSERT_COLS generated constant."""
+    from geneweaver.db.query.publication import PUB_INSERT_COLS
+
+    for idx, value in enumerate(PUB_INSERT_COLS):
+        assert "pub_id" not in str(value)
+        if idx % 2 == 0:
+            assert isinstance(value, Identifier)
+        else:
+            assert isinstance(value, SQL)
+            assert value == SQL(",")
+
+
+def test_pub_id_not_in_pub_insert_cols():
+    """Test the PUB_INSERT_COLS generated constant."""
+    from geneweaver.db.query.publication import PUB_INSERT_COLS
+
+    for value in PUB_INSERT_COLS:
+        assert "pub_id" not in str(value)

tests/unit/query/publication/test_pub_insert_vals.py

@@ -0,0 +1,23 @@
+"""Test the PUB_QUERY generated constant."""
+
+from psycopg.sql import SQL, Placeholder
+
+
+def test_pub_insert_vals_types():
+    """Test the PUB_INSERT_COLS generated constant."""
+    from geneweaver.db.query.publication import PUB_INSERT_VALS
+
+    for idx, value in enumerate(PUB_INSERT_VALS):
+        if idx % 2 == 0:
+            assert isinstance(value, Placeholder)
+        else:
+            assert isinstance(value, SQL)
+            assert value == SQL(",")
+
+
+def test_pub_id_not_in_pub_insert_vals():
+    """Test that the pub_id is not in the PUB_INSERT_VALS constant."""
+    from geneweaver.db.query.publication import PUB_INSERT_VALS
+
+    for value in PUB_INSERT_VALS:
+        assert "pub_id" not in str(value)