From 23cce1afb29b477c1f0f9d4efe7de2c17014a7a4 Mon Sep 17 00:00:00 2001
From: Koncopd <koncopd@gmail.com>
Date: Thu, 21 Nov 2024 16:23:17 +0100
Subject: [PATCH 1/5] add bionty data to gitignore

---
 .gitignore | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.gitignore b/.gitignore
index 291058c..07146bc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,8 @@
+# bionty data
+data/
+sources/
+versions/
+
 # macOS
 .DS_Store
 .AppleDouble

From 86bfb7ac6c4d62dd496a2dceb0ac983b66b3eac7 Mon Sep 17 00:00:00 2001
From: Koncopd <koncopd@gmail.com>
Date: Thu, 21 Nov 2024 16:36:24 +0100
Subject: [PATCH 2/5] use new search

---
 bionty/base/_public_ontology.py | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

diff --git a/bionty/base/_public_ontology.py b/bionty/base/_public_ontology.py
index 12e433b..890f2eb 100644
--- a/bionty/base/_public_ontology.py
+++ b/bionty/base/_public_ontology.py
@@ -561,24 +561,18 @@ def search(
         self,
         string: str,
         *,
-        field: PublicOntologyField | str | None = None,
+        field: PublicOntologyField | str | list[PublicOntologyField | str] = None,
         limit: int | None = None,
         case_sensitive: bool = False,
-        synonyms_field: PublicOntologyField | str | None = "synonyms",
     ):
-        """Search a given string against a PublicOntology field.
+        """Search a given string against a PublicOntology field or fields.
 
         Args:
             string: The input string to match against the field values.
-            field: The PublicOntologyField of the ontology the input string is matching against.
-            top_hit: Return all entries ranked by matching ratios.
-                If True, only return the top match.
-                Defaults to False.
-            limit: Maximum amount of top results to return.
-                   If None, return all results.
-                   Defaults to None.
+            field: The PublicOntologyField or several fileds of the ontology
+                the input string is matching against. Search all fields containing strings by default.
+            limit: Maximum amount of top results to return. If None, return all results.
             case_sensitive: Whether the match is case sensitive.
-            synonyms_field: By default also search against the synonyms (If None, skips search).
 
         Returns:
             Ranked search results.
@@ -590,13 +584,17 @@ def search(
         """
         from lamin_utils._search import search
 
+        if isinstance(field, PublicOntologyField):
+            field = field.name
+        elif field is not None and not isinstance(field, str):
+            field = [f.name if isinstance(f, PublicOntologyField) else f for f in field]
+
         return search(
             df=self._df,
             string=string,
-            field=self._get_default_field(field),
+            field=field,
             limit=limit,
             case_sensitive=case_sensitive,
-            synonyms_field=str(synonyms_field),
         )
 
     def diff(

From d1359359ccbeb14e59690a208a9efdf514465467 Mon Sep 17 00:00:00 2001
From: Koncopd <koncopd@gmail.com>
Date: Thu, 21 Nov 2024 17:09:07 +0100
Subject: [PATCH 3/5] set index in search result

---
 bionty/base/_public_ontology.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/bionty/base/_public_ontology.py b/bionty/base/_public_ontology.py
index 890f2eb..2acbbd7 100644
--- a/bionty/base/_public_ontology.py
+++ b/bionty/base/_public_ontology.py
@@ -589,13 +589,16 @@ def search(
         elif field is not None and not isinstance(field, str):
             field = [f.name if isinstance(f, PublicOntologyField) else f for f in field]
 
-        return search(
+        result = search(
             df=self._df,
             string=string,
             field=field,
             limit=limit,
             case_sensitive=case_sensitive,
         )
+        if "ontology_id" in result.columns:
+            result = result.set_index("ontology_id")
+        return result
 
     def diff(
         self, compare_to: PublicOntology, **kwargs

From a4809fc491cc178ecfd71347c8d7417d3f336998 Mon Sep 17 00:00:00 2001
From: Koncopd <koncopd@gmail.com>
Date: Fri, 22 Nov 2024 16:32:36 +0100
Subject: [PATCH 4/5] add lower bound on lamin-utils

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ac63464..767a525 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,8 @@ classifiers = [
 ]
 dependencies = [
     "lamindb",
-    "lamindb_setup>=0.77.6",
+    "lamindb-setup>=0.77.6",
+    "lamin-utils>=0.13.9",
     "filelock",
     "requests",
     "pyyaml",

From c77d51fc8d0e9425f418c18c7c6a76e3beb03e62 Mon Sep 17 00:00:00 2001
From: Koncopd <koncopd@gmail.com>
Date: Fri, 22 Nov 2024 16:33:54 +0100
Subject: [PATCH 5/5] fix

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 767a525..02ab984 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,8 +17,8 @@ classifiers = [
 ]
 dependencies = [
     "lamindb",
-    "lamindb-setup>=0.77.6",
-    "lamin-utils>=0.13.9",
+    "lamindb_setup>=0.77.6",
+    "lamin_utils>=0.13.9",
     "filelock",
     "requests",
     "pyyaml",