sapiopycommons 2025.4.15a484__tar.gz → 2025.4.17a486__tar.gz

{sapiopycommons-2025.4.15a484 → sapiopycommons-2025.4.17a486}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.4.15a484
+Version: 2025.4.17a486
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>
@@ -17,7 +17,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.10
 Requires-Dist: databind>=4.5
-Requires-Dist: sapiopylib>=2024.5.24.210
+Requires-Dist: sapiopylib>=2025.4.17.264
 Description-Content-Type: text/markdown
 
 

{sapiopycommons-2025.4.15a484 → sapiopycommons-2025.4.17a486}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2025.04.15a484'
+version='2025.04.17a486'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },
@@ -14,7 +14,7 @@ license = "MPL-2.0"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
-        'sapiopylib>=2024.5.24.210', 'databind>=4.5'
+        'sapiopylib>=2025.4.17.264', 'databind>=4.5'
 ]
 classifiers = [
     "Intended Audience :: Developers",

{sapiopycommons-2025.4.15a484 → sapiopycommons-2025.4.17a486}/src/sapiopycommons/eln/experiment_cache.py

@@ -63,7 +63,7 @@ class ExperimentCacheManager:
         self._predefined_fields = {}
 
     def get_experiment_template(self, name: str, active: bool = True, version: int | None = None,
-                                first_match: bool = False) -> ElnTemplate:
+                                first_match: bool = False, public: bool | None = True) -> ElnTemplate:
         """
         Get the experiment template with the given information.
 
@@ -71,6 +71,10 @@ class ExperimentCacheManager:
         :param active: Whether the template is marked as active.
         :param version: The version of the template to get. If None, the latest version will be returned.
         :param first_match: If true, returns the first match found. If false, raises an exception.
+        :param public: Whether the template is public. If true, only pubic templates will be queried. If false, only
+            private templates will be queried. If None, both public and private templates will be queried. Non-public
+            templates do not have a version number, so this will always fail if public is false and a version number is
+            provided.
         :return: The experiment template with the given information.
         """
         if not hasattr(self, "_templates"):
@@ -78,11 +82,11 @@ class ExperimentCacheManager:
             query.active_templates_only = False
             query.latest_version_only = False
             self._templates = self.eln_man.get_template_experiment_list(query)
-        return self._find_template(self._templates, name, active, version, first_match)
+        return self._find_template(self._templates, name, active, version, first_match, public)
 
 
     def get_protocol_template(self, name: str, active: bool = True, version: int | None = None,
-                              first_match: bool = False) -> ProtocolTemplateInfo:
+                              first_match: bool = False, public: bool | None = True) -> ProtocolTemplateInfo:
         """
         Get the protocol template with the given information. Will throw an exception if multiple templates match
         the given information.
@@ -91,6 +95,10 @@ class ExperimentCacheManager:
         :param active: Whether the template is marked as active.
         :param version: The version of the template to get. If None, the latest version will be returned.
         :param first_match: If true, returns the first match found. If false, raises an exception.
+        :param public: Whether the template is public. If true, only pubic templates will be queried. If false, only
+            private templates will be queried. If None, both public and private templates will be queried. Non-public
+            templates do not have a version number, so this will always fail if public is false and a version number is
+            provided.
         :return: The protocol template with the given information.
         """
         if not hasattr(self, "_protocols"):
@@ -98,11 +106,11 @@ class ExperimentCacheManager:
             query.active_templates_only = False
             query.latest_version_only = False
             self._protocols = self.eln_man.get_protocol_template_info_list(query)
-        return self._find_template(self._protocols, name, active, version, first_match)
+        return self._find_template(self._protocols, name, active, version, first_match, public)
 
     @staticmethod
     def _find_template(templates: list[ElnTemplate] | list[ProtocolTemplateInfo], name: str, active: bool,
-                       version: int, first_match: bool) -> ElnTemplate | ProtocolTemplateInfo:
+                       version: int, first_match: bool, public: bool | None) -> ElnTemplate | ProtocolTemplateInfo:
         """
         Find the experiment or protocol template with the given information.
         """
@@ -114,15 +122,22 @@ class ExperimentCacheManager:
                 continue
             if version is not None and template.template_version != version:
                 continue
+            if public is True and template.template_version is None:
+                continue
+            if public is False and template.template_version is not None:
+                continue
             matches.append(template)
         if not matches:
             raise SapioException(f"No template with the name \"{name}\"" +
                                  ("" if version is None else f" and the version {version}") +
                                  f" found.")
-        if not version:
-            return max(matches, key=lambda x: x.template_version)
+        # Only filter for the max version number if any of the matches actually have a version number.
+        versioned_matches = [x for x in matches if x.template_version is not None]
+        if version is None and versioned_matches:
+            return max(versioned_matches, key=lambda x: x.template_version)
         if len(matches) > 1 and not first_match:
-            raise SapioException(f"Multiple templates with the name \"{name}\" found.")
+            raise SapioException(f"Multiple templates with the name \"{name}\" found. Consider setting first_match to "
+                                 f"true, or restrict your search criteria further.")
         return matches[0]
 
     def get_predefined_field(self, field_name: str, data_type: ElnBaseDataType) -> AbstractVeloxFieldDefinition:

{sapiopycommons-2025.4.15a484 → sapiopycommons-2025.4.17a486}/src/sapiopycommons/eln/step_creation.py

@@ -185,6 +185,7 @@ class GlobalDtTableStepCreation(StepCreation):
         self.layout_name = None
         self.extension_types = None
         self.table_columns = None
+        self.field_names = None
         self.show_key_fields = None