🔖 Stage 0.26 (#479)

* ✨ Add diff (#468) * ✨ Use input prompt (#467) * 📝 Update release notes * 📝 Build docs standalone again (#465) * 📝 Build docs standalone again * 📝 Fix docstring * 📝 Consolidate readme * 👷 Strict erroring docs build * 💚 Fix * 📝 Prettify * 📝 Prettier * 📝 Update release notes * 🚸 Case insensitive search (#466) * 📝 Update release notes * 🔖 Release 0.24.2 * ✨ Use input prompt Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: github-actions <[email protected]> Co-authored-by: Alex Wolf <[email protected]> Co-authored-by: Sunny Sun <[email protected]> * ✨ Add diff implementation Signed-off-by: zethson <[email protected]> * ✅ Add more tests Signed-off-by: zethson <[email protected]> * ✨ Add existing entries diff Signed-off-by: zethson <[email protected]> * ✨ Add to repr Signed-off-by: zethson <[email protected]> * Add to guide Signed-off-by: zethson <[email protected]> --------- Signed-off-by: zethson <[email protected]> Co-authored-by: github-actions <[email protected]> Co-authored-by: Alex Wolf <[email protected]> Co-authored-by: Sunny Sun <[email protected]> * 🍱 Include obsolete terms in .df (#481) * 🚚 Fix tests (#482) --------- Signed-off-by: zethson <[email protected]> Co-authored-by: Lukas Heumos <[email protected]> Co-authored-by: github-actions <[email protected]> Co-authored-by: Alex Wolf <[email protected]>
laminlabs · Jul 23, 2023 · 1e5e8c3 · 1e5e8c3
1 parent 77232a9
commit 1e5e8c3
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diff --git a/bionty/__init__.py b/bionty/__init__.py
@@ -51,7 +51,7 @@
 __version__ = "0.25.2"  # denote release candidate for 0.1.0 with 0.1rc1
 
 # prints warning of python versions
-from lamin_logger import py_version_warning
+from lamin_utils import py_version_warning
 
 py_version_warning("3.8", "3.10")
 

diff --git a/bionty/_bionty.py b/bionty/_bionty.py
@@ -1,13 +1,15 @@
 from __future__ import annotations
 
+import logging
 import os
 from functools import cached_property
 from pathlib import Path
 from typing import Dict, Iterable, List, Literal, Optional, Set, Tuple, Union
 
+import numpy as np
 import pandas as pd
-from lamin_logger import logger
-from lamin_logger._lookup import Lookup
+from lamin_utils import logger
+from lamin_utils._lookup import Lookup
 
 from bionty._md5 import verify_md5
 
@@ -103,6 +105,7 @@ def __repr__(self) -> str:
             f"🎯 {self.__class__.__name__}.search(): free text search of terms\n"
             f"🧐 {self.__class__.__name__}.inspect(): check if identifiers are mappable\n"
             f"👽 {self.__class__.__name__}.map_synonyms(): map synonyms to standardized names\n"
+            f"⚖ {self.__class__.__name__}.diff(): difference between two versions\n"
             f"🔗 {self.__class__.__name__}.ontology: Pronto.Ontology object"
         )
         # fmt: on
@@ -374,7 +377,7 @@ def inspect(
             >>> gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
             >>> gene_bt.inspect(gene_symbols, field=gene_bt.symbol)
         """
-        from lamin_logger._inspect import inspect
+        from lamin_utils._inspect import inspect
 
         return inspect(
             df=self._df,
@@ -426,7 +429,7 @@ def map_synonyms(
             >>> gene_symbols = ["A1CF", "A1BG", "FANCD1", "FANCD20"]
             >>> standardized_symbols = gene_bt.map_synonyms(gene_symbols, gene_bt.symbol)
         """
-        from lamin_logger._map_synonyms import map_synonyms
+        from lamin_utils._map_synonyms import map_synonyms
 
         return map_synonyms(
             df=self._df,
@@ -489,7 +492,7 @@ def search(
             >>> celltype_bt = bt.CellType()
             >>> celltype_bt.search("gamma delta T cell")
         """
-        from lamin_logger._search import search
+        from lamin_utils._search import search
 
         return search(
             df=self._df,
@@ -500,6 +503,66 @@ def search(
             synonyms_field=str(synonyms_field),
         )
 
+    def diff(self, compare_to: Bionty, **kwargs) -> Tuple[pd.DataFrame, pd.DataFrame]:
+        """Determines a diff between two Bionty objects' ontologies.
+
+        Args:
+            compare_to: Bionty object that must be of the same class as the calling object.
+            kwargs: Are passed to pd.DataFrame.compare()
+
+        Returns:
+            A tuple of two DataFrames:
+            1. New entries.
+            2. A pd.DataFrame.compare result which denotes all changes in `self` and `other`.
+
+        Examples:
+            >>> import bionty as bt
+            >>> disease_bt_1 = bt.Disease(source="mondo", version="2023-04-04")
+            >>> disease_bt_2 = bt.Disease(source="mondo", version="2023-04-04")
+            >>> new_entries, modified_entries = disease_bt_1.diff(disease_bt_2)
+            >>> print(new_entries.head())
+            >>> print(modified_entries.head())
+        """
+        if not type(self) is type(compare_to):
+            raise ValueError("Both Bionty objects must be of the same class.")
+
+        if not self.source == compare_to.source:
+            raise ValueError("Both Bionty objects must use the same source.")
+
+        if self.version == compare_to.version:
+            raise ValueError("The versions of the Bionty objects must differ.")
+
+        # The 'parents' column (among potentially others) contain Numpy array values.
+        # We transform them to tuples to determine the diff.
+        def _convert_arrays_to_tuples(arr):  # pragma: no cover
+            if isinstance(arr, np.ndarray):
+                return tuple(arr)
+            else:
+                return arr
+
+        for bt_obj in [self, compare_to]:
+            for column in bt_obj.df().columns:
+                if any(isinstance(val, np.ndarray) for val in bt_obj.df()[column]):
+                    bt_obj._df[column] = bt_obj.df()[column].apply(
+                        _convert_arrays_to_tuples
+                    )
+
+        # New entries
+        new_entries = pd.concat([self.df(), compare_to.df()]).drop_duplicates(
+            keep=False
+        )
+
+        # Changes in existing entries
+        common_index = self.df().index.intersection(compare_to.df().index)
+        self_df_common = self.df().loc[common_index]
+        compare_to_df_common = compare_to.df().loc[common_index]
+        modified_entries = self_df_common.compare(compare_to_df_common, **kwargs)
+
+        logging.info(f"{len(new_entries)} new entries were added.")
+        logging.info(f"{len(modified_entries)} entries were modified.")
+
+        return new_entries, modified_entries
+
 
 class BiontyField:
     """Field of a Bionty model."""

diff --git a/bionty/_ontology.py b/bionty/_ontology.py
@@ -67,8 +67,8 @@ def filter_include_id_prefixes(terms: pronto.ontology._OntologyTerms):
 
         df_values = []
         for term in filtered_terms:
-            # skip terms without id or name and obsolete terms
-            if (not term.id) or (not term.name) or term.obsolete:
+            # skip terms without id or name
+            if (not term.id) or (not term.name):
                 continue
 
             # term definition text

diff --git a/bionty/dev/_handle_sources.py b/bionty/dev/_handle_sources.py
@@ -2,7 +2,7 @@
 from typing import Dict, List, Literal, Union
 
 import pandas as pd
-from lamin_logger import logger
+from lamin_utils import logger
 
 from bionty._settings import settings
 from bionty.dev._io import load_yaml, write_yaml
@@ -90,7 +90,6 @@ def parse_sources_yaml(filepath: Union[str, Path] = PUBLIC_SOURCES) -> pd.DataFr
 
     Args:
         filepath: Path to the versions yaml file.
-        return_df: Whether to return a Pandas DataFrame
 
     Returns:
         - entity

diff --git a/bionty/entities/_experimentalfactor.py b/bionty/entities/_experimentalfactor.py
@@ -2,7 +2,7 @@
 from typing import Dict, Literal, Optional
 
 import pandas as pd
-from lamin_logger import logger
+from lamin_utils import logger
 
 from bionty.entities._shared_docstrings import _doc_params, species_removed
 

diff --git a/docs/guide/ontology.ipynb b/docs/guide/ontology.ipynb
@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "053a464e-df2f-4386-b537-4f0a4fb46408",
    "metadata": {},
@@ -23,7 +22,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "1a61c7de",
    "metadata": {},
@@ -88,7 +86,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "4cb4718b",
    "metadata": {},
@@ -107,7 +104,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "58cd007f",
    "metadata": {},
@@ -126,7 +122,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "66ba4cba",
    "metadata": {},
@@ -179,7 +174,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "be4cab83",
    "metadata": {},
@@ -188,7 +182,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "879230a6",
    "metadata": {},
@@ -230,7 +223,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "689b1622",
    "metadata": {},
@@ -279,7 +271,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "9e501882",
    "metadata": {},
@@ -296,6 +287,69 @@
    "source": [
     "lookup.tumor_size"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "76e2e2f9-19c0-46e2-97f6-4487428ed1c3",
+   "metadata": {},
+   "source": [
+    "## Comparing ontology versions"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "afa16569-5f98-41ec-981c-db1b81fbbe91",
+   "metadata": {},
+   "source": [
+    "Bionty provides {func}`bionty.Bionty.diff` to determine a diff between two ontology versions."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f2b7ba3c-6f25-49d2-9dc2-589fee0f0d53",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "disease_bt_old = bt.Disease(source=\"mondo\", version=\"2023-04-04\")\n",
+    "disease_bt_new = bt.Disease(source=\"mondo\", version=\"2023-02-06\")\n",
+    "\n",
+    "new_entries, modified_entries = disease_bt_old.diff(disease_bt_new)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1f7cbe33-b7f3-4c76-b277-3b849ac2ed98",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "new_entries.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "05dfa5e3-a50c-4488-bc86-929fd198c30d",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "modified_entries.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8ff90ce1-d427-43f6-9c22-868878d59a35",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -317,7 +371,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.10.10"
   },
   "vscode": {
    "interpreter": {

diff --git a/pyproject.toml b/pyproject.toml
@@ -15,7 +15,7 @@ classifiers = [
 ]
 dependencies = [
     "pronto>=2.5.4",
-    "lamin_logger>=0.8.0", # don't pin here as it's pinned in lamindb
+    "lamin_utils>=0.9.1", # don't pin here as it's pinned in lamindb
     "pyyaml",
     "pandas",
     "pyarrow",

diff --git a/tests/test_bionty.py b/tests/test_bionty.py
@@ -20,3 +20,32 @@ def test_reset_sources(monkeypatch):
     CURRENT_SOURCES.unlink()
     LOCAL_SOURCES.unlink()
     bt.reset_sources()
+
+
+def test_diff_successful():
+    disease_bt_1 = bt.Disease(source="mondo", version="2023-04-04")
+    disease_bt_2 = bt.Disease(source="mondo", version="2023-02-06")
+
+    new_entries, modified_entries = disease_bt_1.diff(disease_bt_2)
+    assert len(new_entries) == 819
+    assert len(modified_entries) == 249
+
+
+def test_diff_value_errors():
+    # Two different Bionty object types
+    disease_bt = bt.Disease()
+    phenotype_bt = bt.Phenotype()
+    with pytest.raises(ValueError):
+        disease_bt.diff(phenotype_bt)
+
+    # Different sources
+    disease_bt_1 = bt.Disease(source="mondo")
+    disease_bt_2 = bt.Disease(source="doid")
+    with pytest.raises(ValueError):
+        disease_bt_1.diff(disease_bt_2)
+
+    # Same version
+    disease_bt_3 = bt.Disease(source="mondo", version="2023-04-04")
+    disease_bt_4 = bt.Disease(source="mondo", version="2023-04-04")
+    with pytest.raises(ValueError):
+        disease_bt_3.diff(disease_bt_4)