From dfec363c7dac940c17daf50a4c8aea672c55cc9d Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Thu, 3 Aug 2023 11:55:07 -0400
Subject: [PATCH 1/6] repair purge

---
 pyproject.toml                        | 4 ++--
 src/encoded/project/authentication.py | 2 +-
 src/encoded/tests/test_permissions.py | 9 +++++++++
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index aab6b4f5c..f91f6bcef 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,8 +42,8 @@ certifi = ">=2021.5.30"
 chardet = "3.0.4"
 codeguru-profiler-agent = "^1.2.4"
 colorama = "0.3.3"
-dcicsnovault = "8.2.0.1b45"
-dcicutils = "7.5.1.1b0"
+dcicsnovault = "^9.0.0"
+dcicutils = "^7.5.2"
 encoded-core = "^0.0.2"
 elasticsearch = "7.13.4"
 execnet = "1.4.1"
diff --git a/src/encoded/project/authentication.py b/src/encoded/project/authentication.py
index 88875fac6..0ba4c8aa8 100644
--- a/src/encoded/project/authentication.py
+++ b/src/encoded/project/authentication.py
@@ -8,7 +8,7 @@ def login(self, context, request, *, samesite):
 
     def namespaced_authentication_policy_authenticated_userid(self, namespaced_authentication_policy, request,
                                                               set_user_info_property):
-        set_user_info_property = False
+        set_user_info_property = True
         return super().namespaced_authentication_policy_authenticated_userid(namespaced_authentication_policy, request,
                                                                              set_user_info_property)
 
diff --git a/src/encoded/tests/test_permissions.py b/src/encoded/tests/test_permissions.py
index 9a29cd193..361e7748d 100644
--- a/src/encoded/tests/test_permissions.py
+++ b/src/encoded/tests/test_permissions.py
@@ -52,6 +52,15 @@ def consortium_file(testapp, fastq_format, test_consortium):
     return res.json['@graph'][0]
 
 
+class TestAdminPermissions:
+    """ Tests admins can do various actions, including purging items """
+
+    @staticmethod
+    def test_admin_can_purge(testapp, fastq_format):
+        testapp.patch_json(f'/{fastq_format["uuid"]}', {'status': 'deleted'}, status=200)
+        testapp.delete_json(f'/{fastq_format["uuid"]}/?purge=True', {}, status=200)
+
+
 class TestPermissionsHelper:
 
     @staticmethod

From 15a58afac0eaed563863efc106f48799ea3e0ea1 Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Thu, 3 Aug 2023 16:09:39 -0400
Subject: [PATCH 2/6] app specific schema refs

---
 pyproject.toml                          |  2 +-
 src/encoded/tests/test_merge_schemas.py | 23 +++++++++++++++++
 src/encoded/tests/testing_views.py      | 34 +++++++++++++++++++++++++
 3 files changed, 58 insertions(+), 1 deletion(-)
 create mode 100644 src/encoded/tests/test_merge_schemas.py

diff --git a/pyproject.toml b/pyproject.toml
index f91f6bcef..49078c387 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,7 +42,7 @@ certifi = ">=2021.5.30"
 chardet = "3.0.4"
 codeguru-profiler-agent = "^1.2.4"
 colorama = "0.3.3"
-dcicsnovault = "^9.0.0"
+dcicsnovault = "^9.9.0.0b0"
 dcicutils = "^7.5.2"
 encoded-core = "^0.0.2"
 elasticsearch = "7.13.4"
diff --git a/src/encoded/tests/test_merge_schemas.py b/src/encoded/tests/test_merge_schemas.py
new file mode 100644
index 000000000..963f711a0
--- /dev/null
+++ b/src/encoded/tests/test_merge_schemas.py
@@ -0,0 +1,23 @@
+import pytest
+from snovault.schema_utils import load_schema
+from .testing_views import TestingLinkedSchemaField
+
+
+class TestMergedSchemas:
+    """ Class that contains tests that validate $merge refs are correctly resolved within repo
+        and across repos
+    """
+
+    @staticmethod
+    def test_merged_schemas():
+        """ Checks that we can resolve multiple different schema $ref types """
+        schema = load_schema(TestingLinkedSchemaField.schema)
+        props = schema['properties']
+        for key in ['access_key_id', 'file_format', 'title']:
+            assert key in props
+        # check access key id
+        assert props['access_key_id']['comment'] == 'Only admins are allowed to set this value.'
+        # check file_format
+        assert props['file_format']['linkTo'] == 'FileFormat'
+        # check title
+        assert props['title']['description'] == 'A title for the Consortium.'
diff --git a/src/encoded/tests/testing_views.py b/src/encoded/tests/testing_views.py
index 48163dcff..9cd7b4572 100644
--- a/src/encoded/tests/testing_views.py
+++ b/src/encoded/tests/testing_views.py
@@ -62,3 +62,37 @@ class TestingPostPutPatch(Item):
             },
         }
     }
+
+
+@collection(
+    'testing-linked-schema-fields',
+    acl=[
+        (Allow, 'group.submitter', ['add', 'edit', 'view']),
+    ],
+)
+class TestingLinkedSchemaField(Item):
+    item_type = 'testing_linked_schema_field'
+    schema = {
+        'type': 'object',
+        'additionalProperties': False,
+        'properties': {
+            "schema_version": {
+                "type": "string",
+                "pattern": "^\\d+(\\.\\d+)*$",
+                "requestMethod": [],
+                "default": "1",
+            },
+            # link from snovault field
+            'access_key_id': {
+                '$merge': 'snovault:schemas/access_key.json#/properties/access_key_id'
+            },
+            # link from encoded-core field
+            'file_format': {
+                '$merge': 'encoded_core:schemas/file.json#/properties/file_format'
+            },
+            # link from this repo
+            'title': {
+                '$merge': 'encoded:schemas/consortium.json#/properties/title'
+            }
+        }
+    }

From 20b305f88d871aef76c873d96ef432568eaf7664 Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Fri, 4 Aug 2023 09:53:04 -0400
Subject: [PATCH 3/6] fix incompatible changes

---
 src/encoded/schema_formats.py              | 2 +-
 src/encoded/schemas/consortium.json        | 4 ++--
 src/encoded/schemas/submission_center.json | 4 ++--
 src/encoded/server_defaults.py             | 2 +-
 src/encoded/tests/test_schemas.py          | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/encoded/schema_formats.py b/src/encoded/schema_formats.py
index bb4679a25..1e2907429 100644
--- a/src/encoded/schema_formats.py
+++ b/src/encoded/schema_formats.py
@@ -1,6 +1,6 @@
 import re
 from pyramid.threadlocal import get_current_request
-from jsonschema_serialize_fork import FormatChecker
+from snovault.schema_validation import FormatChecker
 from snovault.server_defaults import test_accession
 from .server_defaults import (
     ACCESSION_FACTORY,
diff --git a/src/encoded/schemas/consortium.json b/src/encoded/schemas/consortium.json
index f516a22ea..685a50d07 100644
--- a/src/encoded/schemas/consortium.json
+++ b/src/encoded/schemas/consortium.json
@@ -1,7 +1,7 @@
 {
     "title": "Consortium",
-    "id": "/profiles/consortium.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/consortium.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "required": [
         "name",
         "title"
diff --git a/src/encoded/schemas/submission_center.json b/src/encoded/schemas/submission_center.json
index 1d1ccd1f7..eb0cf52c7 100644
--- a/src/encoded/schemas/submission_center.json
+++ b/src/encoded/schemas/submission_center.json
@@ -1,7 +1,7 @@
 {
     "title": "SubmissionCenter",
-    "id": "/profiles/submission_center.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/submission_center.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "required": [
         "name",
         "title"
diff --git a/src/encoded/server_defaults.py b/src/encoded/server_defaults.py
index c591e3c4d..1efe98e10 100644
--- a/src/encoded/server_defaults.py
+++ b/src/encoded/server_defaults.py
@@ -1,5 +1,5 @@
 from dcicutils.misc_utils import ignored
-from jsonschema_serialize_fork import NO_DEFAULT
+from snovault.schema_validation import NO_DEFAULT
 from snovault.schema_utils import server_default
 from snovault.server_defaults import get_user_resource
 
diff --git a/src/encoded/tests/test_schemas.py b/src/encoded/tests/test_schemas.py
index 78c789dba..91ee29bf5 100644
--- a/src/encoded/tests/test_schemas.py
+++ b/src/encoded/tests/test_schemas.py
@@ -99,7 +99,7 @@ def test_load_schema(schema, master_mixins, registry, testapp):
 
     if schema not in ['namespaces.json', 'mixins.json']:
         # check that schema.id is same as /profiles/schema
-        idtag = loaded_schema['id']
+        idtag = loaded_schema['$id']
         idtag = idtag.replace('/profiles/', '')
         # special case for access_key.json
         if schema == 'access_key.json':

From b55dc78225ad80df8d161510852c578a4798c2c8 Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Mon, 7 Aug 2023 14:20:28 -0400
Subject: [PATCH 4/6] new snovault

---
 Dockerfile     |   2 +-
 poetry.lock    | 205 ++++++++++++++++++++++++++++++++++++++++++++-----
 pyproject.toml |  13 +---
 3 files changed, 191 insertions(+), 29 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index b58058c76..ad6928caa 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -23,7 +23,7 @@ ENV NGINX_USER=nginx \
     NVM_VERSION=v0.39.1 \
     NODE_VERSION=16.14.0
 
-# Configure Python3.7 venv
+# Configure Python3.9 venv
 ENV VIRTUAL_ENV=/opt/venv
 RUN python -m venv /opt/venv
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"
diff --git a/poetry.lock b/poetry.lock
index 449535fec..0521437c8 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -24,6 +24,25 @@ files = [
     {file = "async_timeout-4.0.2-py3-none-any.whl", hash = "sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c"},
 ]
 
+[[package]]
+name = "attrs"
+version = "23.1.0"
+description = "Classes Without Boilerplate"
+category = "main"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
+    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+]
+
+[package.extras]
+cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
+dev = ["attrs[docs,tests]", "pre-commit"]
+docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
+tests = ["attrs[tests-no-zope]", "zope-interface"]
+tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+
 [[package]]
 name = "aws-requests-auth"
 version = "0.4.3"
@@ -865,14 +884,14 @@ test-randomorder = ["pytest-randomly"]
 
 [[package]]
 name = "dcicsnovault"
-version = "8.2.0.1b45"
+version = "10.0.0"
 description = "Storage support for 4DN Data Portals."
 category = "main"
 optional = false
 python-versions = ">=3.8.1,<3.10"
 files = [
-    {file = "dcicsnovault-8.2.0.1b45-py3-none-any.whl", hash = "sha256:86e79026a3108366c1215113eac6cb9c776142370d9c49b6693bd72382eafbc4"},
-    {file = "dcicsnovault-8.2.0.1b45.tar.gz", hash = "sha256:16931980239377e5bfd7b6b55b3870f82e8400ba54ca895cae6d8cc825a1fb97"},
+    {file = "dcicsnovault-10.0.0-py3-none-any.whl", hash = "sha256:0213097a5a812a3f6aee6b9f407dbf56d8ee65517474a183bc8282c03ecbbf83"},
+    {file = "dcicsnovault-10.0.0.tar.gz", hash = "sha256:f74795ed55da550e39bb6a0b2a4deed2d9747197c77e2cba4131f8a10d93d481"},
 ]
 
 [package.dependencies]
@@ -885,7 +904,7 @@ elasticsearch_dsl = ">=7.4.0,<8.0.0"
 future = ">=0.15.2,<1"
 html5lib = ">=1.1"
 humanfriendly = ">=1.44.9,<2.0.0"
-jsonschema_serialize_fork = ">=2.1.1,<3.0.0"
+jsonschema = ">=4.18.4,<5.0.0"
 netaddr = ">=0.8.0,<1"
 passlib = ">=1.7.4,<2.0.0"
 pillow = ">=9.5.0,<10.0.0"
@@ -922,14 +941,14 @@ xlrd = ">=1.0.0,<2.0.0"
 
 [[package]]
 name = "dcicutils"
-version = "7.5.1.1b0"
+version = "7.7.0"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 category = "main"
 optional = false
 python-versions = ">=3.7,<3.10"
 files = [
-    {file = "dcicutils-7.5.1.1b0-py3-none-any.whl", hash = "sha256:b8fcf538089b6619f3c7b2820e341226f064647c8079113e4325ad1e3f84392d"},
-    {file = "dcicutils-7.5.1.1b0.tar.gz", hash = "sha256:a5f2597b5050a53a4fe368ded9420010931c151b3e9c52ccbbe045332c4ca52e"},
+    {file = "dcicutils-7.7.0-py3-none-any.whl", hash = "sha256:bbc6be71a6241641e8fba3827d02a5210b6aafd12381e95a4a2abf57e804ce12"},
+    {file = "dcicutils-7.7.0.tar.gz", hash = "sha256:dd1e028f1c36a0ee9b5972f5d16d8c9bc53c8d80ece69f8ebd73dd2225842448"},
 ]
 
 [package.dependencies]
@@ -1043,24 +1062,23 @@ develop = ["coverage (<5.0.0)", "mock", "pytest (>=3.0.0)", "pytest-cov", "pytes
 
 [[package]]
 name = "encoded-core"
-version = "0.0.2"
+version = "0.0.3"
 description = "Core data models for Park Lab ENCODE based projects"
 category = "main"
 optional = false
 python-versions = ">=3.8.1,<3.10"
 files = [
-    {file = "encoded_core-0.0.2-py3-none-any.whl", hash = "sha256:37d0373c41b9d2de1949bffe8b57494e55e474e4158af6728e2ccdac4330e96b"},
-    {file = "encoded_core-0.0.2.tar.gz", hash = "sha256:ba7ede8abdf09dea79eef7f29d079ad5ad2ee7ec6eb6e7b2b3f57fd668b75da9"},
+    {file = "encoded_core-0.0.3-py3-none-any.whl", hash = "sha256:73c80e63e2202272582c0d57043d170142f2b479a108743e6f306fc542003d0c"},
+    {file = "encoded_core-0.0.3.tar.gz", hash = "sha256:d5d83119d2b5d3d7d4379a584e13b5601509354bf4a0ae6900c3b63005f39266"},
 ]
 
 [package.dependencies]
 awscli = ">=1.25.36"
 boto3 = ">=1.24.36,<2.0.0"
 botocore = ">=1.27.36,<2.0.0"
-dcicsnovault = ">=8.0.1.0b3,<9.0.0.0"
-dcicutils = ">=7.0.0,<8.0.0"
+dcicsnovault = ">=10.0.0,<11.0.0"
+dcicutils = ">=7.7.0,<8.0.0"
 elasticsearch = "7.13.4"
-jsonschema_serialize_fork = ">=2.1.1,<3.0.0"
 plaster-pastedeploy = "0.6"
 psycopg2-binary = ">=2.9.3,<3.0.0"
 PyJWT = ">=2.6.0,<3.0.0"
@@ -1378,16 +1396,42 @@ files = [
 ]
 
 [[package]]
-name = "jsonschema-serialize-fork"
-version = "2.1.1"
-description = "Fork of Julian Berman's jsonschema to include support for serializing defaults"
+name = "jsonschema"
+version = "4.19.0"
+description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema-4.19.0-py3-none-any.whl", hash = "sha256:043dc26a3845ff09d20e4420d6012a9c91c9aa8999fa184e7efcfeccb41e32cb"},
+    {file = "jsonschema-4.19.0.tar.gz", hash = "sha256:6e1e7569ac13be8139b2dd2c21a55d350066ee3f80df06c608b398cdc6f30e8f"},
+]
+
+[package.dependencies]
+attrs = ">=22.2.0"
+jsonschema-specifications = ">=2023.03.6"
+referencing = ">=0.28.4"
+rpds-py = ">=0.7.1"
+
+[package.extras]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=1.11)"]
+
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.7.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+category = "main"
+optional = false
+python-versions = ">=3.8"
 files = [
-    {file = "jsonschema_serialize_fork-2.1.1.tar.gz", hash = "sha256:49b502326ac408729f72c95db018bf0e4d47860e3cd76e944f368f41a5483ed5"},
+    {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
+    {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
 ]
 
+[package.dependencies]
+referencing = ">=0.28.0"
+
 [[package]]
 name = "loremipsum"
 version = "1.0.5"
@@ -2299,6 +2343,22 @@ async-timeout = {version = ">=4.0.2", markers = "python_full_version <= \"3.11.2
 hiredis = ["hiredis (>=1.0.0)"]
 ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)"]
 
+[[package]]
+name = "referencing"
+version = "0.30.2"
+description = "JSON Referencing + Python"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "referencing-0.30.2-py3-none-any.whl", hash = "sha256:449b6669b6121a9e96a7f9e410b245d471e8d48964c67113ce9afe50c8dd7bdf"},
+    {file = "referencing-0.30.2.tar.gz", hash = "sha256:794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0"},
+]
+
+[package.dependencies]
+attrs = ">=22.2.0"
+rpds-py = ">=0.7.0"
+
 [[package]]
 name = "repoze-debug"
 version = "1.1"
@@ -2355,6 +2415,113 @@ files = [
 [package.extras]
 idna2008 = ["idna"]
 
+[[package]]
+name = "rpds-py"
+version = "0.9.2"
+description = "Python bindings to Rust's persistent data structures (rpds)"
+category = "main"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "rpds_py-0.9.2-cp310-cp310-macosx_10_7_x86_64.whl", hash = "sha256:ab6919a09c055c9b092798ce18c6c4adf49d24d4d9e43a92b257e3f2548231e7"},
+    {file = "rpds_py-0.9.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:d55777a80f78dd09410bd84ff8c95ee05519f41113b2df90a69622f5540c4f8b"},
+    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a216b26e5af0a8e265d4efd65d3bcec5fba6b26909014effe20cd302fd1138fa"},
+    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:29cd8bfb2d716366a035913ced99188a79b623a3512292963d84d3e06e63b496"},
+    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:44659b1f326214950a8204a248ca6199535e73a694be8d3e0e869f820767f12f"},
+    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:745f5a43fdd7d6d25a53ab1a99979e7f8ea419dfefebcab0a5a1e9095490ee5e"},
+    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a987578ac5214f18b99d1f2a3851cba5b09f4a689818a106c23dbad0dfeb760f"},
+    {file = "rpds_py-0.9.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.whl", hash = "sha256:bf4151acb541b6e895354f6ff9ac06995ad9e4175cbc6d30aaed08856558201f"},
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 lock-version = "2.0"
 python-versions = ">=3.9.1,<3.10"
-content-hash = "4f8b19950eebeff4454807dfecc04db694f0d7df91a478dda22588d4cf90cd00"
+content-hash = "50a5b716b03be6d603225c24c816a2cd0637b781878dafcdc327d3086c5f5c65"
diff --git a/pyproject.toml b/pyproject.toml
index 49078c387..c5b394111 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -42,17 +42,15 @@ certifi = ">=2021.5.30"
 chardet = "3.0.4"
 codeguru-profiler-agent = "^1.2.4"
 colorama = "0.3.3"
-dcicsnovault = "^9.9.0.0b0"
-dcicutils = "^7.5.2"
-encoded-core = "^0.0.2"
+dcicsnovault = "^10.0.0"
+dcicutils = "^7.7.0"
+encoded-core = "^0.0.3"
 elasticsearch = "7.13.4"
 execnet = "1.4.1"
-# html5lib = "0.9999999"
 humanfriendly = "^1.44.9"
 hupper = "1.5"
 idna = ">=2.10,<3"
 jmespath = "0.9.0"
-jsonschema_serialize_fork = "^2.1.1"
 loremipsum = "1.0.5"
 netaddr = ">=0.8.0,<1"
 openpyxl = "^3.0.7,!=3.0.8"  # a version 3.0.8 appeared but then got withdrawn, for now just pin 3.0.7. try again later.
@@ -77,7 +75,6 @@ pyramid-retry = "^1.0"
 pyramid-tm = "^2.4"
 pyramid_translogger = "^0.1"
 python-dateutil = "^2.8.2"
-# python-magic is presently pinned to 0.4.15 in lockstep with dcicsnovault's requirements. See explanation there.
 python_magic = ">=0.4.24,<1"
 pytz = ">=2021.3"
 rdflib = "^4.2.2"
@@ -88,12 +85,10 @@ requests = "^2.23.0"
 rfc3986 = "^1.4.0"
 rsa = "3.3"
 rutter = ">=0.3,<1"
-# We don't use this directly. It's part of boto3. It slows down solving to pin.
-# s3transfer = ">=0.3.7,<0.4.0"
 sentry-sdk = "^1.5.6"
 simplejson = "^3.17.0"
 SPARQLWrapper = "^1.8.5"
-SQLAlchemy = "1.4.41"  # Pinned because >=1.3.17 is broken for us (circular constraints prevent deletes)
+SQLAlchemy = "1.4.41"
 structlog = ">=19.2.0,<20"
 #submit4dn = "0.9.7"
 subprocess-middleware = "^0.3.0"

From a97ded90256fbc20e7253c862a3c622a35f9dd3e Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Mon, 7 Aug 2023 14:22:19 -0400
Subject: [PATCH 5/6] version, changelog

---
 CHANGELOG.rst  | 12 +++++++++++-
 pyproject.toml |  2 +-
 2 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 457fe1f53..c2ead352a 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,6 +7,13 @@ smaht-portal
 Change Log
 ----------
 
+0.0.6
+=====
+
+* Removes ``jsonschema_serialize_fork``, use new schema draft version
+* Implement ``$merge`` referential schema fields
+
+
 0.0.5
 =====
 
@@ -15,6 +22,7 @@ Change Log
 * Allow testing with ES in GA with smaht-development credentials
 * Build Docker as part of GA
 
+
 0.0.4
 =====
 
@@ -23,6 +31,7 @@ Change Log
 * Update to use Webpack 5
 * Do some light adjustments to be more compatible with Google Analytics 4 down the line
 
+
 0.0.3
 =====
 
@@ -34,9 +43,10 @@ Change Log
 
 * Implement base level permissioning scheme working with ``consortia`` and ``submission_center``
 
+
 0.0.1
 =====
 
 * Initial version
 * TODO: update base.ini, various other ini file templates once new AWS is provisioned
-* TOOD: build GLOBAL_ENV_BUCKET for testing (conftest.py)
\ No newline at end of file
+* TOOD: build GLOBAL_ENV_BUCKET for testing (conftest.py)
diff --git a/pyproject.toml b/pyproject.toml
index c5b394111..017989020 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.0.5"
+version = "0.0.6"
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

From 34ae33b1839984258b91be3b692e147b50fcc924 Mon Sep 17 00:00:00 2001
From: William Ronchetti <wrr33@cornell.edu>
Date: Mon, 7 Aug 2023 16:05:26 -0400
Subject: [PATCH 6/6] verify non admin purge

---
 src/encoded/tests/test_permissions.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/encoded/tests/test_permissions.py b/src/encoded/tests/test_permissions.py
index 361e7748d..ea455d0b9 100644
--- a/src/encoded/tests/test_permissions.py
+++ b/src/encoded/tests/test_permissions.py
@@ -60,6 +60,11 @@ def test_admin_can_purge(testapp, fastq_format):
         testapp.patch_json(f'/{fastq_format["uuid"]}', {'status': 'deleted'}, status=200)
         testapp.delete_json(f'/{fastq_format["uuid"]}/?purge=True', {}, status=200)
 
+    @staticmethod
+    def test_non_admin_cannot_purge(submitter_testapp, fastq_format):
+        submitter_testapp.patch_json(f'/{fastq_format["uuid"]}', {'status': 'deleted'}, status=422)
+        submitter_testapp.delete_json(f'/{fastq_format["uuid"]}/?purge=True', {}, status=403)
+
 
 class TestPermissionsHelper: