tol-sdk 1.7.4__py3-none-any.whl → 1.7.5b2__py3-none-any.whl

tol/validators/tolid.py

@@ -0,0 +1,110 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from dataclasses import dataclass
+from typing import Any, Dict
+
+from tol.core import DataObject, DataSource
+from tol.core import DataSourceError, DataSourceFilter
+from tol.core.validate import Validator
+from tol.sources.tolid import tolid
+
+
+class TolidValidator(Validator):
+    """
+    Validates that a stream of `DataObject` instances
+    contains unique Tol IDs.
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        species_id_field: str
+        specimen_id_field: str
+        error_ignore_field: str
+        error_ignore_value: str
+        warning_detail: str = 'Species not found in Tol ID source'
+
+    __slots__ = ['__config', '__datasource', '__cached_species_id', '__cached_tolids']
+    __config: Config
+    __datasource: DataSource
+    __cached_species_ids: Dict[str, Any]
+    __cached_tolids: Dict[str, Any]
+
+    def __init__(
+        self,
+        config: Config,
+        datasource=tolid(),
+    ) -> None:
+
+        super().__init__()
+
+        self.__config = config
+        self.__datasource = datasource
+        self.__cached_species_ids = {}
+        self.__cached_tolids = {}
+
+    def _validate_data_object(
+        self,
+        obj: DataObject
+    ) -> None:
+        self.__warning_on_species_not_in_tolid(obj=obj)
+        self.__error_on_specimen_id_and_taxon_not_matching_tolid(obj=obj)
+
+    def __warning_on_species_not_in_tolid(
+        self,
+        obj: DataObject,
+    ) -> None:
+
+        obj_species_id = obj.get_field_by_name(self.__config.species_id_field)
+        if self.__config.species_id_field in obj.attributes:
+            try:
+                if obj_species_id not in self.__cached_species_ids:
+                    self.__cached_species_ids[obj_species_id] = (
+                        self.__datasource.get_one('species', obj_species_id) is not None)
+
+            except DataSourceError as e:
+                if e.status_code == 404:
+                    self.__cached_species_ids[obj_species_id] = False
+
+        species_in_tolid = self.__cached_species_ids[obj_species_id]
+        if species_in_tolid is False:
+            self.add_warning(
+                object_id=obj.id,
+                detail=self.__config.warning_detail,
+                field=self.__config.species_id_field,
+            )
+
+    def __error_on_specimen_id_and_taxon_not_matching_tolid(
+        self,
+        obj: DataObject,
+    ) -> None:
+
+        if (obj.get_field_by_name(self.__config.error_ignore_field) is
+                self.__config.error_ignore_value):
+            return
+
+        if self.__config.specimen_id_field in obj.attributes:
+            specimen_id = obj.get_field_by_name(self.__config.specimen_id_field)
+            if specimen_id not in self.__cached_tolids:
+                f = DataSourceFilter()
+                f.and_ = {'specimen_id': {'eq': {'value': specimen_id}}}
+                self.__cached_tolids[specimen_id] = list(self.__datasource.get_list(
+                    object_type='specimen',
+                    object_filters=f
+                ))
+
+            if (len(self.__cached_tolids[specimen_id]) == 0):
+                return
+            else:
+                taxons = set()
+                for tolid_ in self.__cached_tolids[specimen_id]:
+                    taxons.add(str(tolid_.species.id))
+
+                if str(obj.get_field_by_name(self.__config.species_id_field)) not in taxons:
+                    self.add_error(
+                        object_id=obj.id,
+                        detail=f'Specimen ID {specimen_id} does not match Taxon ID '
+                               f'{obj.get_field_by_name(self.__config.species_id_field)}'
+                               'in TolID source',
+                        field=[self.__config.specimen_id_field, self.__config.species_id_field]
+                    )

tol/validators/unique_values.py

@@ -2,6 +2,9 @@
 #
 # SPDX-License-Identifier: MIT
 
+from dataclasses import dataclass
+from typing import Dict, List, Set
+
 from tol.core import DataObject
 from tol.core.validate import Validator
 
@@ -11,23 +14,28 @@ class UniqueValuesValidator(Validator):
     Validates that a stream of `DataObject` instances
     contains unique values for specified keys.
     """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        unique_keys: List[List[str] | str]
+        detail: str = 'Value is not unique'
+        is_error: bool = True
+
+    __slots__ = ['__config', '__duplicates', '__existing_values']
+    __config: Config
+    __duplicates: Dict[str, List[str]]
+    __existing_values: Dict[str, Set]
 
     def __init__(
         self,
-        unique_keys: list[list[str] | str],
-        *,
-        detail: str = 'Value is not unique',
-        is_error: bool = True,
+        config: Config
     ) -> None:
 
         super().__init__()
 
-        self.__keys = unique_keys
-        self.__detail = detail
-        self.__is_error = is_error
-        self.__duplicates: dict[str, list[str]] = {}
-        self.__existing_values: dict[str, set] = {}
-        for key in self.__keys:
+        self.__config = config
+        self.__duplicates = {}
+        self.__existing_values = {}
+        for key in self.__config.unique_keys:
             if isinstance(key, str):
                 self.__existing_values[key] = set()
             elif isinstance(key, list):
@@ -39,13 +47,13 @@ class UniqueValuesValidator(Validator):
         obj: DataObject
     ) -> None:
 
-        for unique_key in self.__keys:
+        for unique_key in self.__config.unique_keys:
             if isinstance(unique_key, list):
                 concat = ''
                 for key in unique_key:
                     concat = concat + '/' + (str(obj.attributes[key]))
                 if concat in self.__existing_values['/'.join(unique_key)]:
-                    self._duplicate_checks(
+                    self.__duplicate_checks(
                         key=key,
                         value=concat
                     )
@@ -54,14 +62,14 @@ class UniqueValuesValidator(Validator):
 
             else:
                 if obj.attributes[unique_key] in self.__existing_values[unique_key]:
-                    self._duplicate_checks(
+                    self.__duplicate_checks(
                         key=unique_key,
                         value=obj.attributes[unique_key]
                     )
                 else:
                     self.__existing_values[unique_key].add(obj.attributes[unique_key])
 
-    def _duplicate_checks(
+    def __duplicate_checks(
         self,
         key: str,
         value: str
@@ -86,15 +94,15 @@ class UniqueValuesValidator(Validator):
         key: str,
     ) -> None:
 
-        if self.__is_error:
+        if self.__config.is_error:
             self.add_error(
                 object_id=obj.id,
-                detail=self.__detail,
+                detail=self.__config.detail,
                 field=key,
             )
         else:
             self.add_warning(
                 object_id=obj.id,
-                detail=self.__detail,
+                detail=self.__config.detail,
                 field=key,
             )

tol/validators/unique_whole_organisms.py

@@ -0,0 +1,109 @@
+# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
+#
+# SPDX-License-Identifier: MIT
+
+from dataclasses import dataclass
+from typing import List
+
+from tol.core import Validator
+from tol.core.data_object import DataObject
+
+
+class UniqueWholeOrganismsValidator(Validator):
+    """
+    Validates an incoming stream of `DataObject` instances.
+    For each data object (sample) not a SYMBIONT, it checks:
+    1. There are no two samples with organism part WHOLE_ORGANISM with the same SPECIMEN_ID
+    2. There are no samples with organism part *not* WHOLE_ORGANISM that have a SPECIMEN_ID
+       the same as a WHOLE_ORGANISM in the manifest.
+    """
+    @dataclass(slots=True, frozen=True, kw_only=True)
+    class Config:
+        symbiont_field: str
+        organism_part_field: str
+        specimen_id_field: str
+
+    __slots__ = ['__config', '__whole_organisms', '__part_organisms']
+    __config: Config
+    __whole_organisms: List[str]
+    __part_organisms: List[str]
+
+    def __init__(self, config: Config) -> None:
+        super().__init__()
+        self.__whole_organisms = []
+        self.__part_organisms = []
+        self.__config = config
+
+    def _validate_data_object(self, obj: DataObject) -> None:
+        # This function uses a bit of a confusing method for its validation, so I'm going to
+        # leave an explanation here as to how it works for anyone who needs to modify it
+        # in the future!
+        #
+        # In the original code to be adapted, two loops were used. The first looped over each
+        # data object whose ORGANISM_PART was 'WHOLE_ORGANISM', adding them to a list. Before it
+        # did this though, it would check to see if the SPECIMEN_ID of this data object was already
+        # contained in said list (to ensure the specimen IDs were unique). In the second loop, the
+        # rest of the data objects (those whose ORGANISM PART was *not* 'WHOLE_ORGANISM') were
+        # looped over, each being checked to see if their SPECIMEN_ID was contained in the list
+        # (the one containing the whole organisms). In all, this ensures that all whole organisms
+        # have unique specimen IDs, and all part organisms do not share the specimen IDs of any of
+        # the whole organisms.
+        #
+        # The issue when adapting this to a Validator to be used in a pipeline, is that this
+        # function only takes in one data object at a time, via a generator (to save needing to
+        # load many into memory at once). The problem this left us with is that we could no longer
+        # achieve the same result by using two passes of the data, as only one pass was feasible.
+        #
+        # So here's what I ended up with. This validator stores the SPECIMEN_IDs of both all of the
+        # whole organisms *and* part organisms. From this, detecting duplicate whole organisms is
+        # the same, but detecting whether a part organism shared the SPECIMEN_ID of a whole
+        # organism now has two separate cases: when the data object passed into this function is
+        # a whole organism, or a part organism. In the case of it being a part organism, a very
+        # similar solution to before can be used: we simply check whether self.__whole_organisms
+        # conatins the same SPECIMEN_ID. However, for the case where the data object is a whole
+        # organism, effectively the inverse is done; it is the self.__part_organisms list that is
+        # checked. This covers all cases:
+        #   1. There are no duplicates, in which case there will never be a time when the same
+        #      SPECIMEN_ID will be in both lists.
+        #   2. A whole organism is checked, then a part organism with the same SPECIMEN_ID is
+        #      checked. In this case, self.__whole_organisms will contain the same SPECIMEN_ID,
+        #      so the duplicate is detected.
+        #   3. A part organism is checked, then a whole organism with the same SPECIMEN_ID is
+        #      checked. In this case, self.__part_organisms will contain the same SPECIMEN_ID,
+        #      so the duplicate is detected.
+        #
+        # From Thomas :)
+
+        # Ensure the data object is not a SYMBIONT, because organism part checks do not apply
+        if obj.attributes.get(self.__config.symbiont_field) != 'SYMBIONT':
+            specimen_id = obj.attributes.get(self.__config.specimen_id_field)
+            if specimen_id is None:
+                return
+
+            organism_part = obj.attributes.get(self.__config.organism_part_field)
+            if organism_part == 'WHOLE_ORGANISM':
+                if specimen_id in self.__whole_organisms:
+                    self.add_error(
+                        object_id=obj.id,
+                        detail='No two whole organisms can have the same Specimen ID',
+                        field=self.__config.specimen_id_field,
+                    )
+                if specimen_id in self.__part_organisms:
+                    self.add_error(
+                        object_id=obj.id,
+                        detail='A whole organism cannot have a Specimen ID already used for'
+                               'a non-whole organism',
+                        field=self.__config.specimen_id_field,
+                    )
+
+                self.__whole_organisms.append(specimen_id)
+            else:
+                if specimen_id in self.__whole_organisms:
+                    self.add_error(
+                        object_id=obj.id,
+                        detail='A non-whole organism cannot have a Specimen ID already used for'
+                               'a whole organism',
+                        field=self.__config.specimen_id_field,
+                    )
+
+                self.__part_organisms.append(specimen_id)

{tol_sdk-1.7.4.dist-info → tol_sdk-1.7.5b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tol-sdk
-Version: 1.7.4
+Version: 1.7.5b2
 Summary: SDK for interaction with ToL, Sanger and external services
 Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
 License: MIT

{tol_sdk-1.7.4.dist-info → tol_sdk-1.7.5b2.dist-info}/RECORD

@@ -4,11 +4,12 @@ tol/markdown.py,sha256=X-ooYUYLkkVS8DyBHYib8d2QBBNMPlBP5_ZQz8-mAYc,570
 tol/actions/__init__.py,sha256=xOj2kvRYv2GWQLqrpL_xhwZUZDwtOBnxb5CZ9qmP-pk,169
 tol/actions/action.py,sha256=HlfUsfVGd2vuNAwD_01yo1i32nh6UNrt_ytcY2ladgM,651
 tol/actions/upsert_action.py,sha256=DnSz1LhHibF0WcK6Qht5eLIGi3PPXc6GSRsd8Y2dZBE,1366
-tol/api_base/__init__.py,sha256=xv9kkAyb1Q5vhKgq6f-JpY7lIAla51U-gIpA5U1OfkA,312
+tol/api_base/__init__.py,sha256=K8Gpp7nEROn4t0JzJwEbiR49C3KI091ZxoljgnpXGac,367
 tol/api_base/action.py,sha256=l3MzD3jSDdYiZs-HCT4YEsXkp34X26k6yWugXrRB2XU,6575
-tol/api_base/blueprint.py,sha256=lyNXgyyZ7kEL5uuIuSNkardFy8ZcDIfftt8c5xiRjyA,19061
+tol/api_base/blueprint.py,sha256=AHCvBUwvXbXtKuRv_MmQNtMrXnVEtdNVZMh-_CMsYY0,19345
 tol/api_base/controller.py,sha256=5Fp2FobjXXPlongu1j7adGJKlSVufW0_jpk_wZIMRa4,26818
-tol/api_base/pipeline_steps.py,sha256=Y7tOwaBBanxAqiUrTpmF6yaLkEJI6o0ELnM-2CaCvHs,5832
+tol/api_base/data_upload.py,sha256=z8Kp4BWQ6q06vT9ZwS8cgedWuGxBwZLkT6xpHk1K008,2939
+tol/api_base/pipeline_steps.py,sha256=Y3rcqQh1w4F0tCxMLGI3H8W3pbl54OWLrUYbBR44Y4A,5850
 tol/api_base/system.py,sha256=c47sbcNaCd3teiJLO-Zwg1cUNvfCvRO4GmKzAMNxZrw,1219
 tol/api_base/auth/__init__.py,sha256=LNbVtQDlzKWzLoCmxAPSIAcM6mlVMnn0Aj9HFUudseo,460
 tol/api_base/auth/asserts.py,sha256=3kHP2yW6HZxevIgeO8Rl3iKovi8WHZcguVbPSFUjawQ,2765
@@ -30,15 +31,15 @@ tol/api_base/misc/list_get_parameters.py,sha256=6DtUgfKPTok3utKPOxceJdwV_ZnJ5nis
 tol/api_base/misc/relation_url.py,sha256=qfo-okp8Gv9-PEDghMfGZ2pHdYbHRhohvA9v3Govtlo,1127
 tol/api_base/misc/stats_parameters.py,sha256=IVpHqUeGQyjuih59jwqT-fIQMCBeESi2T9b4r9i4J28,1721
 tol/api_client/__init__.py,sha256=58SAywuMrIUCBAY9us_d_RLTMnaUTYWWts0LRQC5wLo,187
-tol/api_client/api_datasource.py,sha256=GOHvAmFzrHdux2wxY-MwUbp6eWbbS01L7FvmVyXJVZM,14330
+tol/api_client/api_datasource.py,sha256=9CPNsujgnp__EwkZGwu9ZTmOxSwOldfLraOEQ7GBLng,14490
 tol/api_client/client.py,sha256=gcnX4iCZtjnCC6qylizXxLe3l6xLhME6LEJH0UeW7V4,13979
-tol/api_client/converter.py,sha256=X6VPk4nrvmXF8EOXy36sn1nvPvYTBYKZ66ofxyQbaY8,4681
+tol/api_client/converter.py,sha256=g32fjqga4mC923n95HmQImPuawMfeb9rQcl3ZxUWP2s,4463
 tol/api_client/exception.py,sha256=MkvJaIyRVCzQ2rKOYnCOcT747mpOeQwGJJl3Kkb1BsQ,3999
-tol/api_client/factory.py,sha256=DIYFmFsQlwOCrUfexiEMBN3ovnreMqUFYNU8hcNvSao,3405
+tol/api_client/factory.py,sha256=WGHA5wio4XS8OHqG07DLSVjehOeAsVoVCc5phAIq4H8,3737
 tol/api_client/filter.py,sha256=D49RIai5Yj4CiQvIkgaEIXdw_oSU7CD5cn9SdXWRYXU,1474
-tol/api_client/parser.py,sha256=67GxGyhb5goVhXQqry7-YKvh9YozC_MkQMFiaAeHPKk,5423
+tol/api_client/parser.py,sha256=88Q2RlPwn9JJsSIukC2_yxfaM2AaXjsGuDOESqY7se4,8351
 tol/api_client/validate.py,sha256=9wFZotTJ4fI21BdO5AuMZok0rDQ4s8zM_WojLdVvA0A,3071
-tol/api_client/view.py,sha256=a0TzPtXhJfVv70exJ86BEZv_oaeXDyitKsj6R5sG3wE,6102
+tol/api_client/view.py,sha256=DvhRTA957Fn5vVPByV7e8ngvJaD9DSa5SaJ48ONWQlU,8753
 tol/barcodes/__init__.py,sha256=k9KoBO0xJyxg1kanLrN0E3HuVSbbpfSInGEsWX-8UsY,214
 tol/barcodes/main.py,sha256=QxueF2AdrclIaQuu7W4lb4eF5tU_l-p3UMsDFIYgCfo,6213
 tol/benchling/__init__.py,sha256=9VIL6PBxvZRaBrN1j2Di75MdEY261kEHs_D-lUutIlg,229
@@ -83,24 +84,24 @@ tol/copo/converter.py,sha256=DnJvIysyVLa1b4hIK0o146ruuxKBYhEDN4kxKxl7Uuc,1127
 tol/copo/copo_datasource.py,sha256=DYOkaUOO2bdW1rmblci_rt4nBo_1Kb7ztxnthbkC-hA,5193
 tol/copo/factory.py,sha256=fzYpPxro6M9GHER4uyJ5dugxDobPskc-f6RNZpLc4ZY,2219
 tol/copo/parser.py,sha256=FRPF0DQNbHTN_nrar80V9a_-3AapXqUErB47zEP0VUQ,2863
-tol/core/__init__.py,sha256=svFcEWLhqgA0hLfFkrN9xWaSLqkC2MDHrBSnUjCGYGE,1124
+tol/core/__init__.py,sha256=ifE1Ji2RF-RWNzo3HTsEKfLIpkRrIBNBPKDwpvzPoMk,1149
 tol/core/attribute_metadata.py,sha256=wYD3NXDdStrpkUZoyTUiEpp7c14f7MLIcyooT1G4GEQ,4091
 tol/core/core_converter.py,sha256=Gn4J507BtqDjnOWV2MFRYGz8YElJAKQItmnCrD72s7k,4504
 tol/core/data_loader.py,sha256=k-ET1nIohIz6PcADbEn9Y7k9TupoiBYxKDkcAl_9pGY,14710
-tol/core/data_object.py,sha256=KLPSXpg0OM7NpaHkwzfldaI_4521odqABA8SyLjthII,3770
-tol/core/data_object_converter.py,sha256=YWlwxDUXZjhkVPbIoVtQNP88vLYeX2vO9CZELNHw4Wo,2840
+tol/core/data_object.py,sha256=GxG04JMcICaiHU1rufkhoD8jb9YQLhE0QWlFU2ZkQsM,4241
+tol/core/data_object_converter.py,sha256=zIGcin3jcoswBfsuUe74C2nxpyzvhHkP4_ZwKZWxh_Y,3765
 tol/core/data_source_attribute_metadata.py,sha256=NHvJ_Gmw7-Oej1MoFCohvq4f6emDJ2HF483UmW2Qd_c,4407
 tol/core/data_source_dict.py,sha256=d-hSmoWTwG6IOc0cQTLap1EBslsxYIWGUd3ScSoeH_Q,1705
 tol/core/datasource.py,sha256=e9GaeDPfO_Gs7cgQhmNxCiSDlRNf64reegzFebcMNkA,6303
 tol/core/datasource_error.py,sha256=TqfqaPANG0gishadhA7myCmTO1Fg9u7hVZOvsY6BdAo,1660
 tol/core/datasource_filter.py,sha256=RY2S9kTx0XwdrFRSE2n2GohB9__fKGzFVsZrkN5hzQk,726
 tol/core/datasource_utils.py,sha256=18mwvFmtJL73_mxtFb56rKXZCGCtZFoEb8sWFKn3Yf0,6232
-tol/core/factory.py,sha256=e0jXNS9NJvSrsbKUe9j19CElaSnKIB0j2pPCpcMa8wU,9273
+tol/core/factory.py,sha256=pLLu8l-yK8QaLTt52izMhKZ2VlFHqRQlUHwMaLL6DI4,9156
 tol/core/http_client.py,sha256=05Wa_ySmpm_lC8OkxqXkq6jer0t693GexpaKNQBHufI,2244
 tol/core/relationship.py,sha256=etdyCjLbfi2tgkaqzE6cntpNtTzgT_jOPGeNKmPu5yc,4624
 tol/core/requested_fields.py,sha256=QFNky8QmT1Cmfn42EYPciwbCueJ0DVQNKkP0Vz-_7Jk,6715
 tol/core/session.py,sha256=6AohamIEfB8oV3Z414ishKqmlTgVfUaGYWzvxLgZgM4,3803
-tol/core/validate.py,sha256=84etPczrGDkqdrNnj4GSrPAeKxYcz8qUy5szJa2QRGY,4082
+tol/core/validate.py,sha256=kFRPhgYyeZisGbSXR7S1pmD8jvz_aZ7RX40bT-gD_iA,4083
 tol/core/operator/__init__.py,sha256=ircyLdj45IlaL5k0cDzWHjEr-_66BAx7YRbuEvWF30k,1826
 tol/core/operator/_filterable.py,sha256=61qr-58ZPHWdWl4XKatjW1GPAhN-oqfjRpVtHHkipvA,1238
 tol/core/operator/_writer.py,sha256=eO4qe4myLjScCRnXeILU30MPOLyQiAZbIBQQ_awqB5I,1725
@@ -132,13 +133,13 @@ tol/eln/entities.py,sha256=3-Z4ibZR11zepz5Nw74PnkpxA_HA31FsRUx61FSPYUo,1209
 tol/eln/generators.py,sha256=ghRUiohLakiAcMzGVPJrPxYmdWijs63YxfRTqmKu3Zc,1227
 tol/eln/sanitise.py,sha256=fMj-VrQTnw4zn2X0wnjWQAI8gWAa8RYqNuv23LXQssI,406
 tol/ena/__init__.py,sha256=T3TCqaHpgi2Uk2PjPGu60GaG2V8cTrHJlVLtZfLFhTQ,174
-tol/ena/client.py,sha256=dYrclPK9KSx464DGt0fa3iVy4H5ODBKwPybIHeYggm4,4878
+tol/ena/client.py,sha256=ldmm7Z9_auQf1zVWjsFLXYgbKvGtSHTsr88YO3zfv2Y,6731
 tol/ena/converter.py,sha256=nxbo4IFzzOvKNMq3Aeiw5iDqVWvY33nTngLppjHAoGY,1144
-tol/ena/ena_datasource.py,sha256=paOC7ujzhpPzhK2CAhqy2RdSFFkOFbVd0om6biABy84,8608
-tol/ena/ena_methods.py,sha256=qOStTxao1eMBAyVdTCRKldxLr8rDH5mC-G0GUSfFJFw,8887
+tol/ena/ena_datasource.py,sha256=jEvyUaH4pfFxmdtn6O_PwOdjPz6u80uAT3SLlR2f5nM,8968
+tol/ena/ena_methods.py,sha256=jgpLssZq-F-vgkO-fYu4jrXenmNkdFpFKAY3VKp5HHE,9209
 tol/ena/factory.py,sha256=3IJCmGLo59PWbGmNqmKho5WYG330OjL8SoZYstIwHt4,3423
 tol/ena/filter.py,sha256=UzOx5ivXvA0TY2QuNzFmS-zDPVNnaAx07DMVkAwVsAE,3370
-tol/ena/parser.py,sha256=8ZyGBA6HbhgjxHDTo9NDot5xSbD-4Y7gzPIKzkQT_D8,2648
+tol/ena/parser.py,sha256=Z4YmUnpfLKng4QwmZkLEj1hUfwYb_bqr-DWgF1Gw-EY,3253
 tol/excel/__init__.py,sha256=M0xL9w9Au8kYOLWzFGuijJ7WoZENOMkZ1XV1ephhlDY,229
 tol/excel/excel.py,sha256=rcA-wfXY9R14OfNKS-NX2sn__9gmQ_G8LoUgWseF1Gk,2124
 tol/excel/excel_datasource.py,sha256=nIMvkCZ1edx8djqsVsPTRi6yCfyKc_dIokTpLy16rwY,3091
@@ -147,7 +148,7 @@ tol/flows/__init__.py,sha256=M7iSvnBJs6fJ8M38cW0bYQa9WW0TN8FHAMjIHPDNAJ4,166
 tol/flows/logger.py,sha256=rWXbaknGcPEZRFvC1CiB1qkhFRZsQk435w7VyJ3cpyw,170
 tol/flows/secrets.py,sha256=1mlbsxaahzYRfVAx3XdztHOmUCtDMSJDzHysdbaCtj0,352
 tol/flows/sequencing_submissions.py,sha256=ukz_y5be-BCBN2y3JPQ2EK6b3jwOCh-187j-jnw3EUY,11027
-tol/flows/converters/__init__.py,sha256=t4Y7jldbvi-bVC-oPkQOlFPrcqblYRvX4D6SpnbcqKk,5928
+tol/flows/converters/__init__.py,sha256=Ee1yMFWwsRoG71ZFCsqtNwF45AR8farmV9h3ERrK994,6154
 tol/flows/converters/benchling_entity_to_benchling_worklist_item_converter_factory.py,sha256=PN27fcvN4JLBnLrtPPAot1cWjAwPQHVcIDoMfPDeKzU,1210
 tol/flows/converters/benchling_extraction_to_elastic_extraction_converter.py,sha256=S8pbmIeKlcXrLPRJHYBUGP0-Q7jTOV2QQk2TeA2naWo,1966
 tol/flows/converters/benchling_extraction_to_elastic_sequencing_request_converter.py,sha256=2RiyRvGRSWzpUwEI4p-s0afshJpFUUxPqv2z-nyDSVg,1992
@@ -179,6 +180,8 @@ tol/flows/converters/gap_assembly_to_elastic_assembly_converter.py,sha256=XK-es-
 tol/flows/converters/genome_notes_genome_note_to_elastic_genome_note_converter.py,sha256=AaUWbVTaWU-NXnUQPaPwI41TE7a-nC4zlg-jrWpPT2s,1166
 tol/flows/converters/goat_taxon_to_elastic_species_converter.py,sha256=1NGs9427OdXGsBaMB467nOF7aTlJsUKYCuoSoABw9L4,1074
 tol/flows/converters/grit_issue_to_elastic_curation_converter.py,sha256=XpRpoRn589MxTqEk6zPWGn6tamJiqY9Ctxk8v0q-dvA,3953
+tol/flows/converters/incoming_sample_to_ena_sample_converter.py,sha256=HmGsg-VCE4W9Dl3lAlcNhWfkVYp1d22DZlFoTaFzeqA,5560
+tol/flows/converters/incoming_sample_to_incoming_sample_with_lists_converter.py,sha256=5Fp1_ojsYqvRcKTgXJbyWqetPisi_vtWFcWr6RtGZoA,1504
 tol/flows/converters/informatics_tolid_to_elastic_tolid_converter.py,sha256=VrvtsDTPlc5Xa3K4rcAMHwV4n71zOH7q5EfALLLQ1tI,587
 tol/flows/converters/labwhere_location_to_elastic_sample_update_converter.py,sha256=NJNmG9sCc2WXc-2J5XfCKXhb2sDH82nZUBekd16PHcw,656
 tol/flows/converters/labwhere_location_to_sts_tray_converter.py,sha256=dSBP5HfdvyIGvNQD6bhi0RKvkwhN8jq69g-0hOXUqEg,672
@@ -237,13 +240,11 @@ tol/prefect/factory.py,sha256=mO4KVnaEYMv-ojGJuiencNQMq6PAMU8cIc4QN5Kq8Gw,2208
 tol/prefect/filter.py,sha256=aNVTSmcrbb_4EllcFtBOSPuUGgwE-f-Kd5_an6lREtM,7044
 tol/prefect/prefect_datasource.py,sha256=JXLS4odWNWUu4mgojQogwE28mBTAbj-OQYFxhYNYHnM,8865
 tol/prefect/prefect_object.py,sha256=Nn3Y6ErQnXubX7M-GzRsfLHEzdHwKr5RWCjIJ4FA28U,495
-tol/s3/__init__.py,sha256=AnYM6rWRDJ-AkUBPuIFGrF3wyeh7euwUCiv2-gPy9J4,351
+tol/s3/__init__.py,sha256=L2Aa12NAYjTRr8W_ArJi3z3ME2bUtCf4CG3JDw1MoMk,282
 tol/s3/converter.py,sha256=KylGAQvu1jRYJl4dcYK1IgbFsmHP3JXRI22MX8UzHz4,1023
 tol/s3/factory.py,sha256=rFcRVy4B8KVsUaaHhtpLUE90_hRnixkO2IjnB6-arkc,2163
 tol/s3/parser.py,sha256=EOiPYJ8ZLigAxKGL4cC8r7OGyjGdSMHmJMnDqHSiG_E,1907
 tol/s3/s3_datasource.py,sha256=tSUc78FN1OudpJcQ-7FI4S_LPT5j-BYIcwFaQPDy_VA,2072
-tol/s3/data_upload/__init__.py,sha256=4dkK7MPB0CzkkujFSVj0FzoG5ri_usQ7XaBB81Vc_qE,85
-tol/s3/data_upload/blueprint.py,sha256=rwZAXsHe_AJXAdRZVdUhtJg3P3SxOs_G_0F1eewPuT4,2574
 tol/sciops/__init__.py,sha256=PaC1_5wZhsZlqeYQRMpDeIf9L6Hi0eXs_pHXaWfscAo,131
 tol/sciops/configuration.py,sha256=21ddgHOmhZE1tcE-5_f4KiV-7CUqkF8yXi4iBYPtfmc,1279
 tol/sciops/consumer.py,sha256=Ikl8glrZ0yQKBhegC84vwNj43iK1Ca_SAn_gcyAhbKQ,2137
@@ -293,11 +294,11 @@ tol/sql/exception.py,sha256=8c9KOVVNlLhqKU4CfsnxR7sd-JhEMnCk3TQ-s9JyogM,544
 tol/sql/ext.py,sha256=9oYHxR3IXUaG17BwTLWFJ-CjdgFrlm3AclctZ1FP0MQ,1752
 tol/sql/factory.py,sha256=cfHq1iH6wqqn5fI0yfOm59Tw6KiZqA7yXScCKBXBc1c,3408
 tol/sql/filter.py,sha256=O711DnBG7RssQKwZ76fqA8Vm2IN7pzVrigxc1I2G4-Y,15417
-tol/sql/model.py,sha256=Bi68mEsaWDSFxtouqMJqiG4wL6Ziv4uGo6UB9D8Odd4,12098
+tol/sql/model.py,sha256=MAsQdw4L-SzCWCNQd3UVufxPuXFV3GmREss-ouWfh0U,12091
 tol/sql/relationship.py,sha256=EClMgVx_If5nZV9MV99TQk7Wr7uACWetwQdWAliM5XI,2891
 tol/sql/session.py,sha256=VmqTegr4L2X2zvaOJCpwSrkVRx8fc1RVL0drkL2MXu8,806
 tol/sql/sort.py,sha256=ENrjHGgj4fZtXKmkdlkv1HRi1X14SVlcl-tp8Pu7G0k,2553
-tol/sql/sql_converter.py,sha256=h3vQz65MGeJutumSecUDxLuG403lWpJIKPwMO5ahQPI,4300
+tol/sql/sql_converter.py,sha256=taD5FRwadvw2bBaUGrCIiUs0-ATAbBnRYI1M7xe3yEc,4618
 tol/sql/sql_datasource.py,sha256=jLPQSolGtKRKezjVnMrlj8YO6bLepyiFARMbDYEXuN8,16219
 tol/sql/action/__init__.py,sha256=T1zAsCza_lvsNtXF1ecSLt9OFGup8tGnIs68YylBmXI,142
 tol/sql/action/factory.py,sha256=HkareJp_57ud0_Bdd9Kwz3_Rnq2l211sGJgftohFAHg,3589
@@ -305,7 +306,7 @@ tol/sql/auth/__init__.py,sha256=e3JuwugXmXobklqZ1Mt1w03qPgb1WdUaJVM7oblzHyk,202
 tol/sql/auth/blueprint.py,sha256=u0vT_TC9IMKrg08QFa9W29_83mT0y0jzLj3DvXy1BBw,25906
 tol/sql/auth/models.py,sha256=4xNWBvyGiI3mwRyDY5ty48Bv9178ApQXPR-YjIdCsvk,11879
 tol/sql/pipeline_step/__init__.py,sha256=O7u4RrLfuoB0mwLcPxFoUrdTBZGB_4bE1vWCn5ho-qw,147
-tol/sql/pipeline_step/factory.py,sha256=hrv9iAjdUu3sq6R94PXKclatZNMKY8YMgBDwLWKuvR0,5131
+tol/sql/pipeline_step/factory.py,sha256=E5_Bs1379UGlRajKnb77iPmqhXBMemQR1C53SSPjXB4,5134
 tol/sql/standard/__init__.py,sha256=2NbLXFk0rneGZosZ2ESIRcT0WMK0KncmPWaLPqvX-i4,142
 tol/sql/standard/factory.py,sha256=yY8iWmZRMvUqphwnzBeOIQtKGgxsU6AcA7YTz53UYvc,20010
 tol/status/__init__.py,sha256=sBo-j1wCmberl89uryVCBEJk8ohbfsYhaNpIp_brR9Y,146
@@ -319,15 +320,27 @@ tol/treeval/treeval_datasource.py,sha256=GzY6JwH67b5QdV-UVdCFJfgGAIuZ96J2nl53YxZ
 tol/utils/__init__.py,sha256=764-Na1OaNGUDWpMIu51ZtXG7n_nB5MccUFK6LmkWRI,138
 tol/utils/csv.py,sha256=mihww25fSn72c4h-RFeqD_pFIG6KHZP4v1_C0rx81ws,421
 tol/utils/s3.py,sha256=aoYCwJ-qcMqFrpxmViFqPa0O1jgp0phtztO3-0CSNjw,491
-tol/validators/__init__.py,sha256=bIMjfuRd358nUPLp6fMG9nTs43gM9aA9oY_AINgxkWU,379
-tol/validators/allowed_keys.py,sha256=BJMomJtaQdxsdGsueDtLewv75TlwdIXiQipLGFcJ7_c,1331
-tol/validators/allowed_values.py,sha256=yJ5SdiUlV7PSKORtsBJ9hYSqwvlx_esbFmFL_Gxh-p4,2262
-tol/validators/regex.py,sha256=dKodGH0sv6DbqWeV6QXE6-GYjnG4rMO0rg8IEIaQG60,2364
-tol/validators/regex_by_value.py,sha256=o99NJlWPgQ0GrpVnep8-cHfjWnc9F2rChmXHIxjrMrk,2543
-tol/validators/unique_values.py,sha256=tEXDNJj95XUJdhsZlO-pkXdQz-EYaSG-mcp4MDTL7eY,2835
-tol_sdk-1.7.4.dist-info/licenses/LICENSE,sha256=RF9Jacy-9BpUAQQ20INhTgtaNBkmdTolYCHtrrkM2-8,1077
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-tol_sdk-1.7.4.dist-info/RECORD,,
+tol/validators/__init__.py,sha256=CcamQvWpywu5aXWc1D9CoZAZcbioRBlNUuTX-XOKqQE,1060
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+tol/validators/assert_on_condition.py,sha256=FCzmN2Crhku0bdEpXuKEbDaoU6RbAZCUDUxQ8OHK92M,2017
+tol/validators/ena_checklist.py,sha256=nxoiJWHKDk2HzeJMKgME_KGNYUBSaCx5jbp4yXQMf00,2875
+tol/validators/ena_submittable.py,sha256=ruryfVcQtRJ5JsAFBcVZ_3hzTDwRWGXpdPUAfdrYmWg,1948
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+tol/validators/specimens_have_same_taxon.py,sha256=BrkYXhr1KVnJcDe-PrKXf0AF9740BbFV2XVMrtu98CQ,2167
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tol/s3/data_upload/__init__.py

@@ -1,3 +0,0 @@
-# SPDX-FileCopyrightText: 2025 Genome Research Ltd.
-#
-# SPDX-License-Identifier: MIT