sapiopycommons 2025.8.14a703__py3-none-any.whl → 2026.1.22a847__py3-none-any.whl

sapiopycommons/general/time_util.py

@@ -133,9 +133,10 @@ class TimeUtil:
         return datetime.fromtimestamp(millis / 1000, tz).strftime(time_format)
 
     @staticmethod
-    def format_to_millis(time_point: str, time_format: str, timezone: str | int = None) -> int:
+    def format_to_millis(time_point: str, time_format: str, timezone: str | int = None) -> int | None:
         """
-        Convert the input time from the provided format to milliseconds.
+        Convert the input time from the provided format to milliseconds. If None is passed to the time_point parameter,
+        None will be returned.
 
         :param time_point: The time in some date/time format to convert from.
         :param time_format: The format that the time_point is in. Documentation for how the time formatting works
@@ -144,6 +145,9 @@ class TimeUtil:
             timezone variable set by the TimeUtil. A list of valid timezones can be found at
             https://en.wikipedia.org/wiki/List_of_tz_database_time_zones. May also accept a UTC offset in seconds.
         """
+        if time_point is None:
+            return None
+
         tz = TimeUtil.__to_tz(timezone)
         return int(datetime.strptime(time_point, time_format).replace(tzinfo=tz).timestamp() * 1000)
 
@@ -166,11 +170,12 @@ class TimeUtil:
         return TimeUtil.shift_millis(millis, to_timezone, from_timezone)
 
     @staticmethod
-    def shift_millis(millis: int, to_timezone: str = "UTC", from_timezone: str | None = None) -> int:
+    def shift_millis(millis: int, to_timezone: str = "UTC", from_timezone: str | None = None) -> int | None:
         """
         Take a number of milliseconds for a time in from_timezone and output the epoch timestamp that would display that
         same time in to_timezone. A use case for this is when dealing with static date fields to convert a provided
         timestamp to the value necessary to display that timestamp in the same way when viewed in the static date field.
+        If None is passed to the millis parameter, None will be returned.
 
         :param millis: The time in milliseconds to convert from.
         :param to_timezone: The timezone to shift to. If not provided, uses UTC.
@@ -180,17 +185,21 @@ class TimeUtil:
         :return: The epoch timestamp that would display as the same time in to_timezone as the given time in
             from_timezone.
         """
+        if millis is None:
+            return None
+
         to_offset: int = TimeUtil.__get_timezone_offset(to_timezone) * 1000
         from_offset: int = TimeUtil.__get_timezone_offset(from_timezone) * 1000
         return millis + from_offset - to_offset
 
     @staticmethod
     def shift_format(time_point: str, time_format: str, to_timezone: str = "UTC", from_timezone: str | None = None) \
-            -> int:
+            -> int | None:
         """
         Take a timestamp for a time in from_timezone and output the epoch timestamp that would display that same time
         in to_timezone. A use case for this is when dealing with static date fields to convert a provided timestamp to
         the value necessary to display that timestamp in the same way when viewed in the static date field.
+        If None is passed to the time_point parameter, None will be returned.
 
         :param time_point: The time in some date/time format to convert from.
         :param time_format: The format that the time_point is in. Documentation for how the time formatting works
@@ -202,6 +211,9 @@ class TimeUtil:
         :return: The epoch timestamp that would display as the same time in to_timezone as the given time in
             from_timezone.
         """
+        if time_point is None:
+            return None
+
         millis: int = TimeUtil.format_to_millis(time_point, time_format, from_timezone)
         return TimeUtil.shift_millis(millis, to_timezone, from_timezone)
 
@@ -215,9 +227,192 @@ class TimeUtil:
         :param time_format: The format that the time_point should be in. Documentation for how the time formatting works
             can be found at https://docs.python.org/3.10/library/datetime.html#strftime-and-strptime-behavior
         """
+        if time_point is None:
+            return False
         try:
             # If this function successfully runs, then the time_point matches the time_format.
             TimeUtil.format_to_millis(time_point, time_format, "UTC")
             return True
         except Exception:
             return False
+
+
+MILLISECONDS_IN_A_SECOND: int = 1000
+MILLISECONDS_IN_A_MINUTE: int = 60 * MILLISECONDS_IN_A_SECOND
+MILLISECONDS_IN_AN_HOUR: int = 60 * MILLISECONDS_IN_A_MINUTE
+MILLISECONDS_IN_A_DAY: int = 24 * MILLISECONDS_IN_AN_HOUR
+
+class ElapsedTime:
+    _start: int
+    _end: int
+
+    _total_days: float
+    _total_hours: float
+    _total_minutes: float
+    _total_seconds: float
+    _total_milliseconds: int
+
+    _days: int
+    _hours: int
+    _minutes: int
+    _seconds: int
+    _milliseconds: int
+
+    def __init__(self, start: int | float, end: int | float | None = None):
+        """
+        :param start: The start timestamp in milliseconds (int) or seconds (float).
+        :param end: The end timestamp in milliseconds (int) or seconds (float). If None, uses the current epoch time in
+            milliseconds.
+        """
+        if isinstance(start, float):
+            start = int(start * 1000)
+
+        if end is None:
+            end = TimeUtil.now_in_millis()
+        elif isinstance(end, float):
+            end = int(end * 1000)
+
+        self._start = start
+        self._end = end
+
+        self._total_milliseconds = end - start
+        self._total_seconds = self._total_milliseconds / MILLISECONDS_IN_A_SECOND
+        self._total_minutes = self._total_milliseconds / MILLISECONDS_IN_A_MINUTE
+        self._total_hours = self._total_milliseconds / MILLISECONDS_IN_AN_HOUR
+        self._total_days = self._total_milliseconds / MILLISECONDS_IN_A_DAY
+
+        elapsed: int = end - start
+        self._days: int = elapsed // MILLISECONDS_IN_A_DAY
+        elapsed -= self._days * MILLISECONDS_IN_A_DAY
+        self._hours: int = elapsed // MILLISECONDS_IN_AN_HOUR
+        elapsed -= self._hours * MILLISECONDS_IN_AN_HOUR
+        self._minutes: int = elapsed // MILLISECONDS_IN_A_MINUTE
+        elapsed -= self._minutes * MILLISECONDS_IN_A_MINUTE
+        self._seconds: int = elapsed // MILLISECONDS_IN_A_SECOND
+        elapsed -= self._seconds * MILLISECONDS_IN_A_SECOND
+        self._milliseconds = elapsed
+
+    @staticmethod
+    def as_eta(total: int, progress: int, start: int | float, now: int | float | None = None) -> ElapsedTime:
+        """
+        Calculate the estimated time remaining for a task based on how much time has passed so far and how many items
+        have been completed. The estimated time remaining is calculated by determining the average time per item
+        completed so far and multiplying that by the number of items remaining.
+
+        :param total: The total number of items that need to be completed for the task.
+        :param progress: The number of items that have been completed so far.
+        :param start: The start time of a task in milliseconds (int) or seconds (float).
+        :param now: The amount of time that has passed so far while performing the task in milliseconds (int)
+            or seconds (float). If None, uses the current epoch time in milliseconds.
+        :return: An ElapsedTime object representing the estimated time remaining.
+        """
+        if now is None:
+            now = TimeUtil.now_in_millis()
+        is_int: bool = isinstance(start, int) and isinstance(now, int)
+        # How much time has elapsed so far.
+        elapsed: int | float = now - start
+        # The average time it has taken to complete each record so far.
+        per_record: int | float = (elapsed // progress) if is_int else (elapsed / progress)
+        # The estimated time remaining based on the average time per record.
+        remaining: int | float = (total - progress) * per_record
+        return ElapsedTime(now, now + remaining)
+
+    def __str__(self) -> str:
+        time_str: str = f"{self._hours:02d}:{self._minutes:02d}:{self._seconds:02d}.{self._milliseconds:03d}"
+        if self._days:
+            return f"{self._days}d {time_str}"
+        return time_str
+
+    @property
+    def start(self) -> int:
+        """
+        The start timestamp in milliseconds.
+        """
+        return self._start
+
+    @property
+    def end(self) -> int:
+        """
+        The end timestamp in milliseconds.
+        """
+        return self._end
+
+    @property
+    def total_days(self) -> float:
+        """
+        The total number of days in the elapsed time. For example, an elapsed time of 1.5 days would
+        return 1.5.
+        """
+        return self._total_days
+
+    @property
+    def total_hours(self) -> float:
+        """
+        The total number of hours in the elapsed time. For example, an elapsed time of 1.5 days would
+        return 36.0.
+        """
+        return self._total_hours
+
+    @property
+    def total_minutes(self) -> float:
+        """
+        The total number of minutes in the elapsed time. For example, an elapsed time of 1.5 days would
+        return 2,160.0.
+        """
+        return self._total_minutes
+
+    @property
+    def total_seconds(self) -> float:
+        """
+        The total number of seconds in the elapsed time. For example, an elapsed time of 1.5 days would
+        return 129,600.0.
+        """
+        return self._total_seconds
+
+    @property
+    def total_milliseconds(self) -> int:
+        """
+        The total number of milliseconds in the elapsed time. For example, an elapsed time of 1.5 days would
+        return 129,600,000.
+        """
+        return self._total_milliseconds
+
+    @property
+    def days(self) -> int:
+        """
+        The number of full days in the elapsed time. For example, an elapsed time of 1.5 days would
+        return 1.
+        """
+        return self._days
+
+    @property
+    def hours(self) -> int:
+        """
+        The number of full hours in the elapsed time, not counting full days. For example, an elapsed time of 1.5 days
+        would return 12.
+        """
+        return self._hours
+
+    @property
+    def minutes(self) -> int:
+        """
+        The number of full minutes in the elapsed time, not counting full hours. For example, an elapsed time of
+        1.5 hours would return 30.
+        """
+        return self._minutes
+
+    @property
+    def seconds(self) -> int:
+        """
+        The number of full seconds in the elapsed time, not counting full minutes. For example, an elapsed time of 1
+        minute and 45 seconds would return 45.
+        """
+        return self._seconds
+
+    @property
+    def milliseconds(self) -> int:
+        """
+        The number of milliseconds in the elapsed time, not counting full seconds. For example, an elapsed time of
+        1.25 seconds would return 250.
+        """
+        return self._milliseconds

sapiopycommons/recordmodel/record_handler.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import io
 import warnings
 from collections.abc import Iterable
-from typing import Collection, TypeVar, TypeAlias
+from typing import Collection, TypeVar
 from weakref import WeakValueDictionary
 
 from sapiopycommons.general.aliases import RecordModel, SapioRecord, FieldMap, FieldIdentifier, AliasUtil, \
@@ -31,13 +31,6 @@ from sapiopylib.rest.utils.recordmodel.ancestry import RecordModelAncestorManage
 from sapiopylib.rest.utils.recordmodel.properties import Parents, Parent, Children, Child, ForwardSideLink, \
     ReverseSideLink
 
-# Aliases for longer name.
-_PropertyGetter: TypeAlias = AbstractRecordModelPropertyGetter
-_PropertyAdder: TypeAlias = AbstractRecordModelPropertyAdder
-_PropertyRemover: TypeAlias = AbstractRecordModelPropertyRemover
-_PropertySetter: TypeAlias = AbstractRecordModelPropertySetter
-_PropertyType: TypeAlias = RecordModelPropertyType
-
 # CR-47717: Use TypeVars in the type hints of certain functions to prevent PyCharm from erroneously flagging certain
 # return type hints as incorrect.
 IsRecordModel = TypeVar('IsRecordModel', bound=RecordModel)
@@ -100,6 +93,10 @@ class RecordHandler:
             PyRecordModel instead of a WrappedRecordModel.
         :return: The record model for the input.
         """
+        # PR-47792: Set the wrapper_type to None if a str was provided instead of a type[WrappedType]. The type hints
+        # say this shouldn't be done anyway, but using this as a safeguard against user error.
+        if isinstance(wrapper_type, str):
+            wrapper_type = None
         if wrapper_type is not None:
             self.__verify_data_type(record, wrapper_type)
             if isinstance(record, PyRecordModel):
@@ -642,6 +639,40 @@ class RecordHandler:
         with io.BytesIO(file_data.encode() if isinstance(file_data, str) else file_data) as stream:
             self.dr_man.set_record_image(record, stream)
 
+    def get_file_blob_data(self, record: SapioRecord, field_name: FieldIdentifier) -> bytes:
+        """
+        Retrieve file blob data for a given record from one of its file blob fields.
+
+        :param record: The record model to retrieve from.
+        :param field_name: The name of the file blob field to retrieve the data from.
+        :return: The file bytes of the given record's file blob data for the input field.
+        """
+        record: DataRecord = AliasUtil.to_data_record(record)
+        field_name: str = AliasUtil.to_data_field_name(field_name)
+        with io.BytesIO() as data_sink:
+            def consume_data(chunk: bytes):
+                data_sink.write(chunk)
+
+            self.dr_man.get_file_blob_data(record, field_name, consume_data)
+            data_sink.flush()
+            data_sink.seek(0)
+            file_bytes = data_sink.read()
+        return file_bytes
+
+    def set_file_blob_data(self, record: SapioRecord, field_name: FieldIdentifier, file_name: str, file_data: str | bytes) -> None:
+        """
+        Set the file blob data for a given record on one of its file blob fields.
+
+        :param record: The record model to set the file blob data of.
+        :param field_name: The name of the file blob field to set the data for.
+        :param file_name: The name of the file being stored in the file blob field.
+        :param file_data: The file data of the blob to set on the record.
+        """
+        record: DataRecord = AliasUtil.to_data_record(record)
+        field_name: str = AliasUtil.to_data_field_name(field_name)
+        with io.BytesIO(file_data.encode() if isinstance(file_data, str) else file_data) as stream:
+            self.dr_man.set_file_blob_data(record, field_name, file_name, stream)
+
     @staticmethod
     def sum_of_field(models: Iterable[SapioRecord], field_name: FieldIdentifier) -> float:
         """
@@ -783,7 +814,8 @@ class RecordHandler:
         return [{field_name: value} for value in values]
 
     @staticmethod
-    def get_from_all(records: Iterable[RecordModel], getter: _PropertyGetter[_PropertyType]) \
+    def get_from_all(records: Iterable[RecordModel],
+                     getter: AbstractRecordModelPropertyGetter[RecordModelPropertyType]) \
             -> list[RecordModelPropertyType]:
         """
         Use a getter property on all records in a list of record models. For example, you can iterate over a list of
@@ -798,7 +830,8 @@ class RecordHandler:
         return [x.get(getter) for x in records]
 
     @staticmethod
-    def set_on_all(records: Iterable[RecordModel], setter: _PropertySetter[_PropertyType]) \
+    def set_on_all(records: Iterable[RecordModel],
+                   setter: AbstractRecordModelPropertySetter[RecordModelPropertyType]) \
             -> list[RecordModelPropertyType]:
         """
         Use a setter property on all records in a list of record models. For example, you can iterate over a list of
@@ -813,7 +846,8 @@ class RecordHandler:
         return [x.set(setter) for x in records]
 
     @staticmethod
-    def add_to_all(records: Iterable[RecordModel], adder: _PropertyAdder[_PropertyType]) \
+    def add_to_all(records: Iterable[RecordModel],
+                   adder: AbstractRecordModelPropertyAdder[RecordModelPropertyType]) \
             -> list[RecordModelPropertyType]:
         """
         Use an adder property on all records in a list of record models. For example, you can iterate over a list of
@@ -827,7 +861,8 @@ class RecordHandler:
         return [x.add(adder) for x in records]
 
     @staticmethod
-    def remove_from_all(records: Iterable[RecordModel], remover: _PropertyRemover[_PropertyType]) \
+    def remove_from_all(records: Iterable[RecordModel],
+                        remover: AbstractRecordModelPropertyRemover[RecordModelPropertyType]) \
             -> list[RecordModelPropertyType]:
         """
         Use a remover property on all records in a list of record models. For example, you can iterate over a list of

sapiopycommons/rules/eln_rule_handler.py

@@ -184,4 +184,7 @@ class ElnRuleHandler:
             instead of a model wrapper, then the returned records will be PyRecordModels instead of WrappedRecordModels.
         """
         dt: str = AliasUtil.to_data_type_name(wrapper_type)
+        # PR-47792: Set the wrapper_type to None if a str was provided instead of a type[WrappedType].
+        if isinstance(wrapper_type, str):
+            wrapper_type = None
         return self._rec_handler.wrap_models(self.get_records(dt, entry), wrapper_type)

sapiopycommons/rules/on_save_rule_handler.py

@@ -180,4 +180,7 @@ class OnSaveRuleHandler:
             instead of a model wrapper, then the returned records will be PyRecordModels instead of WrappedRecordModels.
         """
         dt: str = AliasUtil.to_data_type_name(wrapper_type)
+        # PR-47792: Set the wrapper_type to None if a str was provided instead of a type[WrappedType].
+        if isinstance(wrapper_type, str):
+            wrapper_type = None
         return self._rec_handler.wrap_models(self.get_records(dt, record_id), wrapper_type)

sapiopycommons/webhook/webservice_handlers.py

@@ -140,7 +140,7 @@ class AbstractWebserviceHandler(AbstractWebhookHandler):
         # Get the login credentials from the headers.
         auth: str = headers.get("Authorization")
         if auth and auth.startswith("Basic "):
-            credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":")
+            credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":", 1)
             user = self.basic_auth(url, credentials[0], credentials[1])
         elif auth and auth.startswith("Bearer "):
             user = self.bearer_token_auth(url, auth.split("Bearer ")[1])

{sapiopycommons-2025.8.14a703.dist-info → sapiopycommons-2026.1.22a847.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.8.14a703
+Version: 2026.1.22a847
 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>=2025.7.31a279
+Requires-Dist: sapiopylib>=2025.10.7.295
 Description-Content-Type: text/markdown
 
 

sapiopycommons-2026.1.22a847.dist-info/RECORD

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