nmdc-runtime 2.10.0__py3-none-any.whl → 2.11.0__py3-none-any.whl

nmdc_runtime/static/ORCID-iD_icon_vector.svg

@@ -0,0 +1,4 @@
+<svg width="32" height="32" fill="none" xmlns="http://www.w3.org/2000/svg">
+  <path fill-rule="evenodd" clip-rule="evenodd" d="M32 16c0 8.837-7.163 16-16 16-8.838 0-16-7.163-16-16C0 7.162 7.162 0 16 0c8.837 0 16 7.162 16 16Z" fill="#A6CE39"/>
+  <path fill-rule="evenodd" clip-rule="evenodd" d="M18.813 9.637h-5.45v13.9h5.474c4.555 0 7.35-3.378 7.35-6.95 0-1.635-.562-3.372-1.77-4.704-1.215-1.336-3.065-2.246-5.605-2.246ZM18.6 21.3h-2.813v-9.425H18.5c1.823 0 3.12.552 3.96 1.4.842.849 1.252 2.021 1.252 3.312 0 .784-.239 1.967-.993 2.948-.745.969-2.01 1.765-4.119 1.765Zm5.311-4.026c-.251 1.74-1.494 4.276-5.311 4.276h-3.063H18.6c3.817 0 5.06-2.536 5.311-4.276Zm1.812-2.405c-.657-2.601-2.85-4.982-6.91-4.982h-5.2 5.2c4.06 0 6.253 2.38 6.91 4.982Zm.215 1.718ZM8.363 9.675v13.887h2.425V9.675H8.363Zm2.175 13.637H8.612h1.925ZM9.575 8.65c.84 0 1.513-.689 1.513-1.513 0-.823-.673-1.512-1.513-1.512-.838 0-1.512.674-1.512 1.513 0 .823.672 1.512 1.512 1.512Z" fill="#fff"/>
+</svg>

nmdc_runtime/static/README.md

@@ -0,0 +1,5 @@
+# Static
+
+This document contains information about the origins of the other files in this directory.
+
+- `ORCID-iD_icon_vector.svg`: On September 27, 2025, we downloaded this SVG file from ORCID's [Brand Library](https://orcid.filecamp.com/s/o/3CCuLloCl73Knntn/VU19wHSMUnX9TD4R), which we found a link to on the [Brand Guidelines](https://info.orcid.org/brand-guidelines/) page of ORCID's website.

nmdc_runtime/util.py

@@ -2,6 +2,7 @@ import json
 import mimetypes
 import os
 import pkgutil
+from collections import defaultdict
 from collections.abc import Iterable
 from copy import deepcopy
 from datetime import datetime, timezone
@@ -13,11 +14,16 @@ from typing import Callable, List, Optional, Set, Dict
 
 import fastjsonschema
 import requests
+from bson.son import SON
 from frozendict import frozendict
+from linkml_runtime import SchemaView
 from nmdc_schema.get_nmdc_view import ViewGetter
 from pymongo.database import Database as MongoDatabase
 from pymongo.errors import OperationFailure
-from refscan.lib.helpers import identify_references
+from refscan.lib.helpers import (
+    identify_references,
+    get_collection_name_to_class_names_map,
+)
 from refscan.lib.ReferenceList import ReferenceList
 from toolz import merge
 
@@ -308,6 +314,32 @@ def nmdc_schema_view():
     return ViewGetter().get_view()
 
 
+@lru_cache
+def get_class_name_to_collection_names_map(
+    schema_view: SchemaView,
+) -> Dict[str, List[str]]:
+    """
+    Returns a mapping of class names to the names of the collections that can store instances of those classes/types,
+    according to the specified `SchemaView`.
+
+    Example output:
+    ```
+    {
+        "Study": ["study_set"],
+        "Biosample": ["biosample_set"],
+        ...
+    }
+    ```
+    """
+    class_name_to_collection_names = defaultdict(list)
+    for collection_name, class_names in get_collection_name_to_class_names_map(
+        schema_view
+    ).items():
+        for class_name in class_names:
+            class_name_to_collection_names[class_name].append(collection_name)
+    return class_name_to_collection_names
+
+
 @lru_cache
 def nmdc_database_collection_instance_class_names():
     names = []
@@ -362,6 +394,12 @@ def all_docs_have_unique_id(coll) -> bool:
 
 
 def specialize_activity_set_docs(docs):
+    """
+    TODO: Document this function.
+
+    TODO: Check whether this function is still necessary, given that the `Database` class
+          in `nmdc-schema` does not have a slot named `activity_set`.
+    """
     validation_errors = {}
     type_collections = get_type_collections()
     if "activity_set" in docs:
@@ -445,6 +483,49 @@ def populated_schema_collection_names_with_id_field(mdb: MongoDatabase) -> List[
     return [n for n in collection_names if mdb[n].find_one({"id": {"$exists": True}})]
 
 
+def does_collection_have_unique_index_on_id_field(
+    collection_name: str, db: MongoDatabase
+) -> bool:
+    """Check whether the specified MongoDB collection has a unique index on its `id` field (not `_id`).
+
+    Note: If the specified MongoDB collection either does not exist or is a _view_ instead of a collection,
+          this function will return `False`.
+
+    References:
+    - https://pymongo.readthedocs.io/en/stable/api/pymongo/collection.html#pymongo.collection.Collection.list_indexes
+    - https://pymongo.readthedocs.io/en/stable/api/pymongo/collection.html#pymongo.collection.Collection.index_information
+    """
+    # Check whether the specified collection actually exists in the database; and, if it does,
+    # whether it is really a _collection_ (as opposed to being a _view_). If it doesn't exist,
+    # or it is a view, return `False` right away.
+    collection_infos_cursor = db.list_collections(filter={"name": collection_name})
+    collection_infos = list(collection_infos_cursor)
+    if len(collection_infos) == 0:
+        return False
+    collection_info = collection_infos[0]
+    if collection_info["type"] != "collection":
+        return False
+
+    # Now that we know we're dealing with a collection, get information about each of its indexes.
+    collection = db.get_collection(collection_name)
+    for index_information in collection.list_indexes():
+        # Get the "field_name-direction" pairs that make up this index.
+        field_name_and_direction_pairs: SON = index_information["key"]
+
+        # If this index involves a number of fields other than one, skip it.
+        # We're only interested in indexes that involve the `id` field by itself.
+        if len(field_name_and_direction_pairs.keys()) != 1:
+            continue
+
+        # Check whether the field this index involves is the `id` field,
+        # and whether this index is `unique`.
+        field_name = list(field_name_and_direction_pairs.keys())[0]
+        if field_name == "id" and index_information.get("unique", False):
+            return True
+
+    return False
+
+
 def ensure_unique_id_indexes(mdb: MongoDatabase):
     """Ensure that any collections with an "id" field have an index on "id"."""
 
@@ -459,6 +540,11 @@ def ensure_unique_id_indexes(mdb: MongoDatabase):
         if collection_name.startswith("system."):  # reserved by mongodb
             continue
 
+        # If the collection already has a unique index on `id`, there's no need
+        # to check anything else about the collection.
+        if does_collection_have_unique_index_on_id_field(collection_name, mdb):
+            continue
+
         if (
             collection_name in schema_collection_names_with_id_field()
             or all_docs_have_unique_id(mdb[collection_name])

nmdc_runtime-2.11.0.dist-info/METADATA

@@ -0,0 +1,46 @@
+Metadata-Version: 2.4
+Name: nmdc-runtime
+Version: 2.11.0
+Summary: A runtime system for NMDC data management and orchestration
+Project-URL: Changelog, https://github.com/microbiomedata/nmdc-runtime/releases
+Project-URL: Documentation, https://docs.microbiomedata.org/runtime
+Project-URL: Issues, https://github.com/microbiomedata/nmdc-runtime/issues
+Project-URL: Repository, https://github.com/microbiomedata/nmdc-runtime
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: base32-lib
+Requires-Dist: boto3
+Requires-Dist: click
+Requires-Dist: dagit
+Requires-Dist: dagster
+Requires-Dist: dagster-graphql
+Requires-Dist: dagster-postgres
+Requires-Dist: fastapi>=0.115.0
+Requires-Dist: fastjsonschema
+Requires-Dist: frozendict
+Requires-Dist: git-root
+Requires-Dist: jq
+Requires-Dist: jsonasobj2
+Requires-Dist: linkml
+Requires-Dist: linkml-runtime
+Requires-Dist: lxml
+Requires-Dist: nmdc-schema==11.11.1
+Requires-Dist: ontology-loader==0.2.2
+Requires-Dist: pandas
+Requires-Dist: passlib[bcrypt]
+Requires-Dist: pydantic[email]>=1.10.0
+Requires-Dist: pyinstrument
+Requires-Dist: pymongo
+Requires-Dist: python-dotenv
+Requires-Dist: python-jose[cryptography]
+Requires-Dist: python-multipart>=0.0.18
+Requires-Dist: pyyaml
+Requires-Dist: refscan==0.3.2
+Requires-Dist: requests
+Requires-Dist: requests-cache
+Requires-Dist: scalar-fastapi<2.0.0,>=1.4.1
+Requires-Dist: tenacity
+Requires-Dist: toolz
+Requires-Dist: tqdm
+Requires-Dist: unidecode
+Requires-Dist: uvicorn[standard]

{nmdc_runtime-2.10.0.dist-info → nmdc_runtime-2.11.0.dist-info}/RECORD

@@ -1,14 +1,15 @@
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 nmdc_runtime/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/config.py,sha256=fVxcqdXv13Fa9CSRPnFIsfmvmlos8o4SFUZcmsXfX_8,2020
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 nmdc_runtime/main.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/mongo_util.py,sha256=L6UxK_6f0wQw2NTKCUVKCp-QLhBudQczDLUdF5odbP8,2943
-nmdc_runtime/util.py,sha256=4-LndkMcQox9fKDfqYkNMU1aKrRVkxhk_7U9L2Kdfno,17644
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 nmdc_runtime/api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/api/analytics.py,sha256=DyxHYCLlpG-IyOvlcLoyurqWgTT2MoiliC06JkZ3aAY,2416
-nmdc_runtime/api/main.py,sha256=KN8sjesJumLn3fRtyOlLrTFknPgQf8XPerO0FuVFPKo,14734
+nmdc_runtime/api/analytics.py,sha256=Vp-BYQZ_sqR282FLLkGUoxlieSqyXxU0DmMvjDzMVsI,3723
+nmdc_runtime/api/entrypoint.sh,sha256=y3lZU2xPnZ3cAVK7tn0Nw-qVGElryt9fzj1IaZ5kkGw,209
+nmdc_runtime/api/main.py,sha256=WnpM-abWDLbxj5mT116UO_45xiO7ec0LQ2ZhGdZhE78,16649
 nmdc_runtime/api/middleware.py,sha256=GUVN26Ym9H87gaxrBs0NAMpOoA7qQfv-7UnIJOkcQkI,1703
-nmdc_runtime/api/openapi.py,sha256=ABjwttrVOwEShYHI6zEkJEVyzKo9D040wpbaKLBubaM,9753
+nmdc_runtime/api/openapi.py,sha256=8E522L6zvhtfM_-eyTNE_Z7EwVvLQh54QUhvvSO5bj0,10159
 nmdc_runtime/api/boot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/api/boot/capabilities.py,sha256=9Cp_yULUeEXN7Nz-WC5XJXTaB7fhOWOCGp8mx050qgg,291
 nmdc_runtime/api/boot/object_types.py,sha256=JL6OZw34lKkbKJJXDIiswfLmn1tkOng4ZKF6ypqWKhs,4382
@@ -16,32 +17,32 @@ nmdc_runtime/api/boot/triggers.py,sha256=fLM588CBYft_no1ENN13XSO6Cj4DB90ZKJl-1Ug
 nmdc_runtime/api/boot/workflows.py,sha256=UpOAMjVKagat-PCKPx7HuriLTnCbhj0EVgpk7UuLpQQ,3826
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-nmdc_runtime/api/core/idgen.py,sha256=jedXPPRVMq4MR3hXK67JkLE6O_BYjOPrP-mv2Fx81CI,5898
+nmdc_runtime/api/core/idgen.py,sha256=ru9nAczRAEp1Koq8yXLCMdkN39dNvfTrIwWwVI2SeWo,8101
 nmdc_runtime/api/core/metadata.py,sha256=AMX-EWfyOU_xobIlDf98PTQLuNCbZuyCPCIELKAoMIk,27943
 nmdc_runtime/api/core/util.py,sha256=OGE9kCui-wEfkfdUeUOBNeqmHJ5fNpJepBo0ivYkMnE,3232
 nmdc_runtime/api/db/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/api/db/mongo.py,sha256=jnig92qWDuiiY0de_l-khg7GMkPYvPVBaC_bISSUH4U,20371
+nmdc_runtime/api/db/mongo.py,sha256=9TfgCTvAmaKp6C7a9AkUTqkYTMYYzyM4na2Ying2ip0,19988
 nmdc_runtime/api/db/s3.py,sha256=tRFEjjVXHMiUdZtRiq1ImvLza2s86TkgubDw3kchDOA,1046
 nmdc_runtime/api/endpoints/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/api/endpoints/capabilities.py,sha256=AkSh8wcsVSOkkjH0kzcM2TcO2o8AuKyXGt1km_VgwVs,717
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-nmdc_runtime/api/endpoints/ids.py,sha256=fuWNP9x_oVPh-VrrrkFT_wtPo-rBTDRr7dOqr1dxAt4,6713
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 nmdc_runtime/api/endpoints/jobs.py,sha256=waQk3A7gGIqcr2GNNX988Bxbvx5bxq-kGKmWXeNBrpY,5010
 nmdc_runtime/api/endpoints/metadata.py,sha256=Msj7k5DxXUzXCZWcvy91T7AIFj1chhn_53Dsc44_qmc,9886
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 nmdc_runtime/api/endpoints/object_types.py,sha256=dTbl3A9j9lyk186arA7cszTEKOY7vXWJO_aKYfFAV8s,1179
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 nmdc_runtime/api/endpoints/runs.py,sha256=PWoEKCFQhWgpWklmRUjTc0UZCvDAa1i59gnPhAcZirA,3326
 nmdc_runtime/api/endpoints/search.py,sha256=_h30mu8_Xndjggg3IllMDn5h8k92BX0ubxqRO85R0Ss,1187
-nmdc_runtime/api/endpoints/sites.py,sha256=wQ0uTDHfKg1nMArE6KNNZHCUljGM6uSlW6nsIGVKDfg,7138
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 nmdc_runtime/api/endpoints/triggers.py,sha256=1DG2oEOV7zu5bT2qoeHrLNajY6K6sEGi7O7po3Bcmbk,673
 nmdc_runtime/api/endpoints/users.py,sha256=syu_Tz05k-OAsDMhe125ofqeiCkmDMjdbRlfvRZ5_rI,7816
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 nmdc_runtime/api/endpoints/workflows.py,sha256=HWTnt-yrHp2DcrQT8BS_-SRQWNibkKNPVOpwqjS9QCA,14383
 nmdc_runtime/api/endpoints/lib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/api/endpoints/lib/helpers.py,sha256=E6pH0NtzKiSGBgIfoeukH5qeHKtxjLtCvw4F8LOacTQ,13874
+nmdc_runtime/api/endpoints/lib/linked_instances.py,sha256=eGBStkzI4bNHqFi1wILQ0JtfolC3h1dFWd8zGDeXdXY,7226
 nmdc_runtime/api/endpoints/lib/path_segments.py,sha256=4nIy_KrYvTc80Np3ELnT94VCk2QfR-2055fMlcbBSPw,5724
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 nmdc_runtime/api/models/capability.py,sha256=4__rqgLS4MCMjbaCM3e_ncR9KW001Klm34p2t_bp65k,262
@@ -59,60 +60,46 @@ nmdc_runtime/api/models/run.py,sha256=OhWBc6lQeEM-GSgUpvJCE2xbZQzv8kdPsEkWlL0xol
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+nmdc_runtime/api/swagger_ui/swagger_ui.py,sha256=lGl4sF7MXsWbX7fiauDPKUOVSVag_WeH7ja5J_KBHg0,1887
+nmdc_runtime/api/swagger_ui/assets/custom-elements.js,sha256=0bxUleZpdRbjFB0t0Tmg3-ReGKfnK6r3bUGjr7zW5UQ,23972
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 nmdc_runtime/minter/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/minter/bootstrap.py,sha256=5Ej6pJVBRryRIi0ZwEloY78Zky7iE2okF6tPwRI2axM,822
 nmdc_runtime/minter/config.py,sha256=-E1kQXTDraabrN4CENuVCHcNJafjVdiHWeUrucxBzMQ,2741
 nmdc_runtime/minter/adapters/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/minter/adapters/repository.py,sha256=XxUVD_csKR0tM7yJT2psXc7WSj1t-tM50JSMfYA9Euo,8281
+nmdc_runtime/minter/adapters/repository.py,sha256=CVVRdGclIDBgbqaOSmSl7OkOSE43kt6zJpE-etXIkOs,9267
 nmdc_runtime/minter/domain/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/minter/domain/model.py,sha256=Ex1ADUZCOXpDoTWb6THRjlZxeDcvvsfsFqkkbiJpUsc,2823
+nmdc_runtime/minter/domain/model.py,sha256=k1n3O3GYfhmFdjU_oHadVTeUIxORQf-VPW4Xy6S5SCQ,3599
 nmdc_runtime/minter/entrypoints/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/minter/entrypoints/fastapi_app.py,sha256=I_lgExs6g1MRpMQdpedrnYdA1L7r_TBi4RiiD8ogrkM,4015
 nmdc_runtime/site/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/graphs.py,sha256=ngDeTTZZWCHUuId3rqjMUF7RpeFNIx2F2Wp_fuy0DE0,17676
-nmdc_runtime/site/ops.py,sha256=dPlOQg9hNTYWDsVK7UKVkRazZkph06k7uyLRSn5l3BY,60870
-nmdc_runtime/site/repository.py,sha256=BCZjaYdI2zyc28OlQm4vkz1w13D34eXtNMqINPMjMAk,44025
-nmdc_runtime/site/resources.py,sha256=dLNtNa4FfSKN_6b21eItn-i8e0ZHyveoBsexl2I6zmo,20144
+nmdc_runtime/site/dagster.yaml,sha256=VCFx2naLjaNzP8AYr5uvzxRIf4fC0mHm7cctcYsVrNA,1204
+nmdc_runtime/site/entrypoint-daemon.sh,sha256=kTc9dQqzR0eQ9TBZcOeeYRXBOKRe05A1INRFes-z3hw,513
+nmdc_runtime/site/entrypoint-dagit-readonly.sh,sha256=ZY-K3l6apK8jA4mjcxePsjWb4_rh-WKz3CHmvvK_zj0,549
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+nmdc_runtime/site/graphs.py,sha256=KeC6SKFNUW6SGubruFRrZsfBRN6tUfc3tp6tEst8bMU,17910
+nmdc_runtime/site/ops.py,sha256=RainLCYEvgglHqgwJWdHu4C15W3DxKOx428vxZSIK_Q,62974
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+nmdc_runtime/site/resources.py,sha256=474u5BvwKubW-oMlQNTXQ9nJTh8dU-Sr_L9k7VhYt_s,20756
 nmdc_runtime/site/util.py,sha256=4h0X_fhjf3HdX6XDR8GvHgkrpxQY4OnZVtaOeXJVxJQ,1935
+nmdc_runtime/site/workspace.yaml,sha256=RCw5i-v0T9MWuEZE-y1vEIJz6x2bpm1fyxheLxLEVLk,431
 nmdc_runtime/site/backup/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/site/backup/nmdcdb_mongodump.py,sha256=My2ORKVIk_Z9wzfnIuamDe3_hv4viid9ToSJDC5J4mY,2689
 nmdc_runtime/site/backup/nmdcdb_mongoexport.py,sha256=y1x3B4-qxF5_itXOKYaix99OvDhW_PYxhLoLc4Y5E1M,4028
 nmdc_runtime/site/backup/nmdcdb_mongoimport.py,sha256=k6w5yscMNYoMBVkaAA9soWS0Dj2CB0FRBSFlifRO3Ro,1739
 nmdc_runtime/site/changesheets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/site/changesheets/base.py,sha256=lZT6WCsEBl-FsTr7Ki8_ploT93uMiVyIWWKM36aOrRk,3171
-nmdc_runtime/site/drsobjects/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/drsobjects/ingest.py,sha256=pcMP69WSzFHFqHB9JIL55ePFhilnCLRc2XHCQ97w1Ik,3107
-nmdc_runtime/site/drsobjects/registration.py,sha256=D1T3QUuxEOxqKZIvB5rkb_6ZxFZiA-U9SMPajyeWC2Y,3572
+nmdc_runtime/site/changesheets/data/OmicsProcessing-to-catted-Biosamples.tsv,sha256=lfAaAhnEOBbXoGmGhVoxbbJRnUOLDtWrF6ycAOtsJFg,128790
+nmdc_runtime/site/changesheets/scripts/missing_neon_soils_ecosystem_data.py,sha256=w7025ohUmoWxYHAl4zTFaV_Ig-CWkeeiZGlEs2J57mc,11628
+nmdc_runtime/site/changesheets/scripts/neon_soils_add_ncbi_ids.py,sha256=OfaVAlhtd7DbH3Y5jHMGnDgOobWel4FnL3tP5BGJqaA,7969
 nmdc_runtime/site/export/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-nmdc_runtime/site/export/ncbi_xml.py,sha256=W686Fufs0UynnvzcQf3qHzgCa4ToynTqo5ZnRU0p514,29690
-nmdc_runtime/site/export/ncbi_xml_utils.py,sha256=XaJZWxxgE-x1t5NUUGpuijryQifzjIs185nw4BmpF7Y,10693
+nmdc_runtime/site/export/ncbi_xml.py,sha256=kDRIv_0eeXfXlpTmK6PbvQYHd1bS69fa3RfE5XpLeIM,54933
+nmdc_runtime/site/export/ncbi_xml_utils.py,sha256=HkE3Iufoqe-9rc6gOVVaqxpz7j98O5idL027w624UwA,15423
 nmdc_runtime/site/export/study_metadata.py,sha256=yR5pXL6JG8d7cAtqcF-60Hp7bLD3dJ0Rut4AtYc0tXA,4844
 nmdc_runtime/site/normalization/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/site/normalization/gold.py,sha256=iISDD4qs4d6uLhv631WYNeQVOzY5DO201ZpPtxHdkVk,1311
@@ -124,15 +111,18 @@ nmdc_runtime/site/translation/neon_benthic_translator.py,sha256=CMoC56ymA0DKPkzq
 nmdc_runtime/site/translation/neon_soil_translator.py,sha256=MMntFXwK62PdPNGpurTq5L3-pct7xAmUymRE2QqMPso,38572
 nmdc_runtime/site/translation/neon_surface_water_translator.py,sha256=_-KDZzC30dQ1y57lXEKWXE6ZfGozNHxGFvbGaj4f0Lg,30536
 nmdc_runtime/site/translation/neon_utils.py,sha256=d00o7duKKugpLHmsEifNbp4WjeC4GOqcgw0b5qlCg4I,5549
-nmdc_runtime/site/translation/submission_portal_translator.py,sha256=x9iUxPxZeWi2ajISBAY09bwzNugqqxkKmuOPw7887v0,41822
+nmdc_runtime/site/translation/submission_portal_translator.py,sha256=351ZfV-SleRAlKEufntP68xYl_oE4b-SeFnHgMpoB1g,45284
 nmdc_runtime/site/translation/translator.py,sha256=kVmDIVfxQ0ry6obAc_SyvlEcPwPCupYeKenRylZWWbI,3643
 nmdc_runtime/site/validation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/site/validation/emsl.py,sha256=OG20mv_3E2rkQqTQtYO0_SVRqFb-Z_zKCiAVbty6Wl0,671
 nmdc_runtime/site/validation/gold.py,sha256=Z5ZzYdjERbrJ2Tu06d0TDTBSfwaFdL1Z23Rl-YkZ2Ow,803
 nmdc_runtime/site/validation/util.py,sha256=Fz3c7dOEKOiYXssitYb50uUI1yRx3wJzFBl0s95Za7s,3632
-nmdc_runtime-2.10.0.dist-info/licenses/LICENSE,sha256=VWiv65r7gHGjgtr3jMJYVmQny5GRpQ6H-W9sScb1x70,2408
-nmdc_runtime-2.10.0.dist-info/METADATA,sha256=y7q8IQWm8basdnSM6ZZL3BraYycLH54QdUT80Cfoupw,11885
-nmdc_runtime-2.10.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-nmdc_runtime-2.10.0.dist-info/entry_points.txt,sha256=JxdvOnvxHK_8046cwlvE30s_fV0-k-eTpQtkKYA69nQ,224
-nmdc_runtime-2.10.0.dist-info/top_level.txt,sha256=b0K1s09L_iHH49ueBKaLrB5-lh6cyrSv9vL6x4Qvyz8,13
-nmdc_runtime-2.10.0.dist-info/RECORD,,
+nmdc_runtime/static/NMDC_logo.svg,sha256=-13FrhQMWOg7FMprd3p6dwSOEf8xWkrHJB_P-nxGvLw,40570
+nmdc_runtime/static/ORCID-iD_icon_vector.svg,sha256=JOKAW7lAn7Giws6aS_jBQGYG4DoPUBQ5S5mgmCSwmcA,973
+nmdc_runtime/static/README.md,sha256=g0fitEFvZfBcSWzgjOxzDdfouBlq95xFKpAag0VPzL4,397
+nmdc_runtime/static/favicon.ico,sha256=FsOefOmgCU9fp2f1FxKimZ8zHg7mBYj_Cv70S5VIcuI,15086
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+nmdc_runtime-2.11.0.dist-info/entry_points.txt,sha256=JxdvOnvxHK_8046cwlvE30s_fV0-k-eTpQtkKYA69nQ,224
+nmdc_runtime-2.11.0.dist-info/licenses/LICENSE,sha256=VWiv65r7gHGjgtr3jMJYVmQny5GRpQ6H-W9sScb1x70,2408
+nmdc_runtime-2.11.0.dist-info/RECORD,,

{nmdc_runtime-2.10.0.dist-info → nmdc_runtime-2.11.0.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any
-

nmdc_runtime/api/endpoints/ids.py

@@ -1,192 +0,0 @@
-"""
-`router` here is deprecated in favor of `nmdc_runtime.minter.entrypoints.fastapi_app.router`
-"""
-
-import re
-from typing import List, Dict, Any
-
-from fastapi import APIRouter, Depends, HTTPException
-from pydantic import ValidationError
-from pymongo.database import Database as MongoDatabase
-from starlette import status
-from toolz import dissoc
-
-from nmdc_runtime.api.core.idgen import (
-    generate_ids,
-    decode_id,
-    collection_name,
-)
-from nmdc_runtime.api.core.util import raise404_if_none, pick
-from nmdc_runtime.api.db.mongo import get_mongo_db
-from nmdc_runtime.api.models.id import (
-    MintRequest,
-    pattern_shoulder,
-    AssignedBaseName,
-    pattern_assigned_base_name,
-    IdBindingRequest,
-    pattern_base_object_name,
-    IdThreeParts,
-    pattern_naa,
-)
-from nmdc_runtime.api.models.site import get_current_client_site, Site
-
-router = APIRouter()
-
-
-@router.post("/ids/mint", response_model=List[str])
-def mint_ids(
-    mint_req: MintRequest,
-    mdb: MongoDatabase = Depends(get_mongo_db),
-    site: Site = Depends(get_current_client_site),
-):
-    """Generate one or more identifiers.
-
-    Leaving `populator` blank will set it to the site ID of the request client.
-    """
-    ids = generate_ids(
-        mdb,
-        owner=site.id,
-        populator=(mint_req.populator or site.id),
-        number=mint_req.number,
-        naa=mint_req.naa,
-        shoulder=mint_req.shoulder,
-    )
-    return ids
-
-
-@router.post("/ids/bindings", response_model=List[Dict[str, Any]])
-def set_id_bindings(
-    binding_requests: List[IdBindingRequest],
-    mdb: MongoDatabase = Depends(get_mongo_db),
-    site: Site = Depends(get_current_client_site),
-):
-    bons = [r.i for r in binding_requests]
-    ids: List[IdThreeParts] = []
-    for bon in bons:
-        m = re.match(pattern_base_object_name, bon)
-        ids.append(
-            IdThreeParts(
-                naa=m.group("naa"),
-                shoulder=m.group("shoulder"),
-                blade=m.group("blade"),
-            )
-        )
-    # Ensure that user owns all supplied identifiers.
-    for id_, r in zip(ids, binding_requests):
-        collection = mdb.get_collection(collection_name(id_.naa, id_.shoulder))
-        doc = collection.find_one({"_id": decode_id(str(id_.blade))}, ["__ao"])
-        if doc is None:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=f"id {r.i} not found",
-            )
-        elif doc.get("__ao") != site.id:
-            raise HTTPException(
-                status_code=status.HTTP_403_FORBIDDEN,
-                detail=(
-                    f"authenticated site client does not manage {r.i} "
-                    f"(client represents site {site.id}).",
-                ),
-            )
-    # Ensure no attempts to set reserved attributes.
-    if any(r.a.startswith("__a") for r in binding_requests):
-        raise HTTPException(
-            status_code=status.HTTP_403_FORBIDDEN,
-            detail="Cannot set attribute names beginning with '__a'.",
-        )
-    # Process binding requests
-    docs = []
-    for id_, r in zip(ids, binding_requests):
-        collection = mdb.get_collection(collection_name(id_.naa, id_.shoulder))
-
-        filter_ = {"_id": decode_id(id_.blade)}
-        if r.o == "purge":
-            docs.append(collection.find_one_and_delete(filter_))
-        elif r.o == "rm":
-            docs.append(collection.find_one_and_update(filter_, {"$unset": {r.a: ""}}))
-        elif r.o == "set":
-            docs.append(collection.find_one_and_update(filter_, {"$set": {r.a: r.v}}))
-        elif r.o == "addToSet":
-            docs.append(
-                collection.find_one_and_update(filter_, {"$addToSet": {r.a: r.v}})
-            )
-        else:
-            # Note: IdBindingRequest root_validator methods should preclude this.
-            raise HTTPException(
-                status_code=status.HTTP_400_BAD_REQUEST, detail="Invalid operation 'o'."
-            )
-
-        return [dissoc(d, "_id") for d in docs]
-
-
-@router.get("/ids/bindings/{rest:path}", response_model=Dict[str, Any])
-def get_id_bindings(
-    rest: str,
-    mdb: MongoDatabase = Depends(get_mongo_db),
-):
-    cleaned = rest.replace("-", "")
-    parts = cleaned.split(":")
-    if len(parts) != 2:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=(
-                "Invalid ID - needs both name assigning authority (NAA) part"
-                "(e.g. 'nmdc') and name part (e.g. 'fk4ra92'), separated by a colon (':')."
-            ),
-        )
-    naa = parts[0]
-    suffix_parts = parts[1].split("/")
-    if len(suffix_parts) == 2 and suffix_parts[-1] != "":  # one '/', or ends with '/'
-        assigned_base_name, attribute = suffix_parts
-    else:
-        assigned_base_name = suffix_parts[0]
-        attribute = None
-
-    if re.match(pattern_naa, naa) is None:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=f"Invalid ID - invalid name assigning authority (NAA) '{naa}'.",
-        )
-    print(assigned_base_name)
-    if re.match(pattern_shoulder, assigned_base_name) is None:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail=(
-                "Invalid ID - invalid shoulder. "
-                "Every name part begins with a 'shoulder', a "
-                "sequence of letters followed by a number, "
-                "for example 'fk4'. "
-                "Did you forget to include the shoulder?",
-            ),
-        )
-    try:
-        m = re.match(pattern_assigned_base_name, AssignedBaseName(assigned_base_name))
-        shoulder, blade = m.group("shoulder"), m.group("blade")
-        id_decoded = decode_id(blade)
-    except (AttributeError, ValidationError):
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="Invalid ID - characters used outside of base32.",
-        )
-    except ValueError:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail="Invalid ID - failed checksum. Did you copy it incorrectly?",
-        )
-
-    collection = mdb.get_collection(collection_name(naa, shoulder))
-    d = raise404_if_none(collection.find_one({"_id": id_decoded}))
-    d = dissoc(d, "_id")
-    if attribute is not None:
-        if attribute not in d:
-            raise HTTPException(
-                status_code=status.HTTP_404_NOT_FOUND,
-                detail=(
-                    f"attribute '{attribute}' not found in "
-                    f"{naa}:{assigned_base_name}."
-                ),
-            )
-        rv = pick(["where", attribute], d)
-    else:
-        rv = d
-    return rv

nmdc_runtime/containers.py

@@ -1,14 +0,0 @@
-"""Containers module."""
-
-from dependency_injector import containers, providers
-
-from nmdc_runtime.domain.users.userService import UserService
-from nmdc_runtime.infrastructure.database.impl.mongo.models.user import (
-    UserQueries,
-)
-
-
-class Container(containers.DeclarativeContainer):
-    user_queries = providers.Singleton(UserQueries)
-
-    user_service = providers.Factory(UserService, user_queries=user_queries)

nmdc_runtime/core/db/Database.py

@@ -1,13 +0,0 @@
-from contextlib import contextmanager
-
-from motor import motor_asyncio
-
-
-class Database:
-    def __init__(self, db_url: str) -> None:
-        self._client = motor_asyncio.AsyncIOMotorClient(db_url)
-        self._db = self._client["database"]
-
-    @contextmanager
-    def session(self):
-        return self._db

nmdc_runtime/core/exceptions/__init__.py

@@ -1,23 +0,0 @@
-from .base import (
-    CustomException,
-    BadRequestException,
-    NotFoundException,
-    ForbiddenException,
-    UnprocessableEntity,
-    DuplicateValueException,
-    UnauthorizedException,
-)
-from .token import DecodeTokenException, ExpiredTokenException
-
-
-__all__ = [
-    "CustomException",
-    "BadRequestException",
-    "NotFoundException",
-    "ForbiddenException",
-    "UnprocessableEntity",
-    "DuplicateValueException",
-    "UnauthorizedException",
-    "DecodeTokenException",
-    "ExpiredTokenException",
-]